diff --git a/tools/adapter_removal/.lint_skip b/tools/adapter_removal/.lint_skip
deleted file mode 100644
index 2092d1d0d68..00000000000
--- a/tools/adapter_removal/.lint_skip
+++ /dev/null
@@ -1 +0,0 @@
-TestsCaseValidation
diff --git a/tools/adapter_removal/adapter_removal.xml b/tools/adapter_removal/adapter_removal.xml
index 103f65b7d24..e706ed434d7 100644
--- a/tools/adapter_removal/adapter_removal.xml
+++ b/tools/adapter_removal/adapter_removal.xml
@@ -244,9 +244,11 @@ $fastq_merging_options.collapse_conservatively
         </data>
     </outputs>
     <tests>
-        <!-- Single dataset input, all defaults -->
+        <!-- Test 01: Single dataset input, all defaults -->
         <test expect_num_outputs="2">
-            <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
+            <conditional name="input_type_cond">
+                <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
+            </conditional>
             <output name="output_settings" ftype="txt">
                 <assert_contents>
                     <has_size value="2117" delta="10"/>
@@ -264,11 +266,13 @@ $fastq_merging_options.collapse_conservatively
                 </assert_contents>
             </output>
        </test>
-        <!-- Dataset pair input, all defaults -->
+        <!-- Test 02: Dataset pair input, all defaults -->
         <test expect_num_outputs="3">
-            <param name="input_type" value="pair"/>
-            <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
-            <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
+            <conditional name="input_type_cond">
+                <param name="input_type" value="pair"/>
+                <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
+                <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
+            </conditional>
             <section name="fastq_options">
                 <param name="convert_uracils" value="false"/>
                 <param name="mask_degenerate_bases" value="true"/>
@@ -298,12 +302,14 @@ $fastq_merging_options.collapse_conservatively
                 </assert_contents>
             </output>
        </test>
-        <!-- Dataset pair input, all defaults, interleaved output -->
+        <!-- Test 03: Dataset pair input, all defaults, interleaved output -->
         <test expect_num_outputs="2">
-            <param name="input_type" value="pair"/>
-            <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
-            <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
-            <param name="interleaved_output" value="yes"/>
+            <conditional name="input_type_cond">
+                <param name="input_type" value="pair"/>
+                <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
+                <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
+                <param name="interleaved_output" value="yes"/>
+            </conditional>
             <output name="output_settings" ftype="txt">
                 <assert_contents>
                     <has_size value="2593" delta="10"/>
@@ -321,15 +327,17 @@ $fastq_merging_options.collapse_conservatively
                 </assert_contents>
             </output>
        </test>
-        <!-- Collection of dataset pairs input, all defaults -->
+        <!-- Test 04: Collection of dataset pairs input, all defaults -->
         <test expect_num_outputs="3">
-            <param name="input_type" value="paired"/>
-            <param name="reads_collection">
-                <collection type="paired">
-                    <element name="forward" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
-                    <element name="reverse" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
-                </collection>
-            </param>
+            <conditional name="input_type_cond">
+                <param name="input_type" value="paired"/>
+                <param name="reads_collection">
+                    <collection type="paired">
+                        <element name="forward" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
+                        <element name="reverse" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
+                    </collection>
+                </param>
+            </conditional>
             <output name="output_settings" ftype="txt">
                 <assert_contents>
                     <has_size value="2594" delta="10"/>
@@ -355,11 +363,13 @@ $fastq_merging_options.collapse_conservatively
                 </assert_contents>
             </output>
        </test>
-        <!-- Dataset pair input, all defaults, all optional outputs checked -->
+        <!-- Test 05: Dataset pair input, all defaults, all optional outputs checked -->
         <test expect_num_outputs="7">
-            <param name="input_type" value="pair"/>
-            <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
-            <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
+            <conditional name="input_type_cond">
+                <param name="input_type" value="pair"/>
+                <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
+                <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
+            </conditional>
             <param name="output_select" value="output_singleton,output_collapsed,output_collapsed_truncated,output_discarded"/>
             <output name="output_settings" ftype="txt">
                 <assert_contents>
diff --git a/tools/aegean/.lint_skip b/tools/aegean/.lint_skip
deleted file mode 100644
index f530e93cdd0..00000000000
--- a/tools/aegean/.lint_skip
+++ /dev/null
@@ -1,2 +0,0 @@
-TestsCaseValidation
-TestsParamInInputs
diff --git a/tools/aegean/gaeval.xml b/tools/aegean/gaeval.xml
index 4456d172f18..a6a019b0b33 100644
--- a/tools/aegean/gaeval.xml
+++ b/tools/aegean/gaeval.xml
@@ -1,5 +1,5 @@
-<tool id="aegean_gaeval" name="AEGeAn GAEVAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
-    <description> compute coverage and integrity scores for gene models using transcript alignments.</description>
+<tool id="aegean_gaeval" name="AEGeAn GAEVAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description> compute coverage and integrity scores for gene models using transcript alignments</description>
     <macros>                                                                                           
         <import>macros.xml</import>
     </macros>
@@ -9,57 +9,35 @@
     <version_command>gaeval --version</version_command>
     <command detect_errors="exit_code">
         <![CDATA[
-            gaeval "$alignmentgff3" "$genesgff3" 
+            gaeval '$alignmentgff3' '$genesgff3' 
             -a $weights.alpha
             -b $weights.beta
             -g $weights.gamma
             -e $weights.epsilon
             -c $expected.expcds
             -5 $expected.exp5putr
-            -3 $expected.exp3putr > "$output"
+            -3 $expected.exp3putr > '$output'
             ]]>
     </command>
     <inputs>
-        <param name="alignmentgff3" type="data" format="gff3" label="Alignment GFF3 file" />
+        <param name="alignmentgff3" type="data" format="gff3" label="Alignment GFF3 file"/>
         <param name="genesgff3" type="data" format="gff3" label="Genes GFF3 file"/>
         <!-- Weight options -->
-        <section name="weights"
-            title="Weights for calculating integrity score"
-            expanded="False">
-            <param argument="--alpha" type="float"                
-                min="0" max="1" value="0.6" 
-                label="Introns confirmed, or % expected CDS lenght for single-exon genes"   
-                help="The percentage of introns confirmed by an alignment gap; for single-exon gene predictions lacking introns, it represents the ratio of the observed CDS length to the expected CDS length. "/>
-            <param argument="--beta" type="float"                
-                min="0" max="1" value="0.3" 
-                label="Exon coverage"   
-                help="Overall percentage of individual exons spanned by at least one sequencing read."/>
-            <param argument="--gamma" type="float" 
-                min="0" max="1" value="0.05"
-                label="% expected 5’ UTR length"
-                help="The ratio of the observed 5’ UTR length to the expected 5’ UTR length."/>
-            <param argument="--epsilon" type="float" 
-                min="0" max="1" value="0.05"
-                label="% expected 3’ UTR lenght"
-                help="The ratio of the observed 3’ UTR length to the expected 3’ UTR length."/>
+        <section name="weights" title="Weights for calculating integrity score" expanded="False">
+            <param argument="--alpha" type="float" min="0" max="1" value="0.6" label="Introns confirmed, or % expected CDS lenght for single-exon genes" help="The percentage of introns confirmed by an alignment gap; for single-exon gene predictions lacking introns, it represents the ratio of the observed CDS length to the expected CDS length"/>
+            <param argument="--beta" type="float" min="0" max="1" value="0.3" label="Exon coverage" help="Overall percentage of individual exons spanned by at least one sequencing read."/>                
+            <param argument="--gamma" type="float" min="0" max="1" value="0.05" label="% expected 5’ UTR length" help="The ratio of the observed 5’ UTR length to the expected 5’ UTR length."/>
+            <param argument="--epsilon" type="float" min="0" max="1" value="0.05" label="% expected 3’ UTR lenght" help="The ratio of the observed 3’ UTR length to the expected 3’ UTR length."/>
         </section>
         <!-- Expected feature lenght options -->
-        <section name="expected"
-            title="Expected feature lenghts for calculating integrity score"
-            expanded="False">
-            <param name="expcds" type="integer"
-                min="0" max="1000" value="400"
-                label="Expected CDs length (in bp) (-c)" />
-            <param name="exp5putr" type="integer" 
-                min="0" max="1000" value="200"
-                label="Expected 5’ UTR length (-5)" />
-            <param name="exp3putr" type="integer"
-                min="0" max="1000" value="100" 
-                label="Expected 3’ UTR length (-3)" />
+        <section name="expected" title="Expected feature lenghts for calculating integrity score" expanded="False">
+            <param name="expcds" type="integer" min="0" max="1000" value="400" label="Expected CDs length (in bp) (-c)"/>
+            <param name="exp5putr" type="integer" min="0" max="1000" value="200" label="Expected 5’ UTR length (-5)"/>
+            <param name="exp3putr" type="integer" min="0" max="1000" value="100" label="Expected 3’ UTR length (-3)"/>
         </section>
     </inputs>
     <outputs>
-        <data name="output" format="tabular" />
+        <data name="output" format="tabular"/>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
@@ -74,7 +52,7 @@
                 <param name="alpha" value="0.5"/>
                 <param name="beta" value="0.4"/>
                 <param name="gamma" value="0.05"/>
-                <param name="epsion" value="0.05"/>
+                <param name="epsilon" value="0.05"/>
             </section>
             <output name="output" file="gaeval_output_test2.txt"/>
         </test>
@@ -88,7 +66,6 @@
             </section>
             <output name="output" file="gaeval_output_test3.txt" lines_diff="2"/>
         </test>
-
     </tests>
     <help>
         <![CDATA[
diff --git a/tools/aegean/locuspocus.xml b/tools/aegean/locuspocus.xml
index 61546a3e94d..9e6119c2524 100644
--- a/tools/aegean/locuspocus.xml
+++ b/tools/aegean/locuspocus.xml
@@ -1,4 +1,4 @@
-<tool id="aegean_locuspocus" name="AEGeAn LocusPocus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+<tool id="aegean_locuspocus" name="AEGeAn LocusPocus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description> calculate locus coordinates for the given gene annotation</description>
     <macros>                                                                                           
         <import>macros.xml</import>
@@ -41,66 +41,38 @@
             ]]>
     </command>
     <inputs>
-        <param name="genesgff3" type="data" format="gff3" label="GFF3 File" />
+        <param name="genesgff3" type="data" format="gff3" label="GFF3 File"/>
         <section name="ilocus_parsing" title="iLocus parsing options" expanded="True">
-            <param argument="--delta" type="integer" 
-                min="0" max="1000" value="500"
-                label="Gene loci extension"
-                help="When parsing interval loci, use the following delta to extend gene loci and include potential regulatory regions" />
+            <param argument="--delta" type="integer" min="0" max="1000" value="500" label="Gene loci extension" help="When parsing interval loci, use the following delta to extend gene loci and include potential regulatory regions"/>
             <param name="mode" type="select" label="Annotation mode">
                 <option value="" selected="true">Default mode</option>
                 <option value="--skipends"> Exclude unannotated iLoci at either end of the sequence</option>
                 <option value="--endsonly"> Report only incomplete iLocus fragments at the unannotated ends of sequences</option>
             </param>
-            <param argument="--skipiloci"  type="boolean"            
-                truevalue="--skipiiloci" falsevalue=""
-                label="Do not report intergenic iLoci" />
+            <param argument="--skipiloci"  type="boolean" truevalue="--skipiiloci" falsevalue="" label="Do not report intergenic iLoci"/>
         </section>
         <section name="refine_options" title="Refine options" expanded="false">
             <conditional name="refine_parameters">
-                <param name="refine" type="select" 
-                    label="Mode for handling of overlpping genes"
-                    help="Refine mode allows for a more nuanced handling of overlapping genes.">
+                <param name="refine" type="select" label="Mode for handling of overlpping genes" help="Refine mode allows for a more nuanced handling of overlapping genes.">
                     <option value="">Default</option>
                     <option value="--refine">Refine mode</option>
                 </param>
                 <when value=""/>
                 <when value="--refine">
-                    <param argument="--cds" type="boolean" 
-                        truevalue="--cds" falsevalue=""
-                        label="Use CDS rather than UTRs"
-                        help="(-c)" />
+                    <param argument="--cds" type="boolean" truevalue="--cds" falsevalue="" label="Use CDS rather than UTRs" help="(-c)"/>
                 </when>
             </conditional>
-            <param argument="--minoverlap" type="integer" 
-                max="20" min="1" value="1" 
-                label="Minimum number of overlapping nucleotides"
-                help="The minimum number of nucleotides two genes must overlap to be grouped in the same iLocus" />
+            <param argument="--minoverlap" type="integer" max="20" min="1" value="1" label="Minimum number of overlapping nucleotides" help="The minimum number of nucleotides two genes must overlap to be grouped in the same iLocus"/>
         </section>
         <section name="input_options" title="Input options" expanded="false">
-            <param  argument="--filter" type="text" 
-                value="gene"
-                label="Comma-separated list of feature types to use"
-                help="Select the featured used to annotate intervals on a genome (e.g. gene, intron, exon)." />
-            <param argument="--parent" type="text" 
-                value="" optional="true"
-                label="Create a parent for features that lack a parent feature"
-                help="If a feature of type $CT exists without a parent, create a parent for this feature with type $PT; for example, mRNA:gene will create a gene feature  as a parent for any top-level mRNA feature."/>
-            <param argument="--pseudo" type="boolean" 
-                truevalue="--pseudo" falsevalue=""
-                label="Correct erroneously labeled pseudogenes"/>   
+            <param argument="--filter" type="text" value="gene" label="Comma-separated list of feature types to use" help="Select the featured used to annotate intervals on a genome (e.g. gene, intron, exon)."/>
+            <param argument="--parent" type="text" value="" optional="true" label="Create a parent for features that lack a parent feature" help="If a feature of type $CT exists without a parent, create a parent for this feature with type $PT; for example, mRNA:gene will create a gene feature  as a parent for any top-level mRNA feature."/>
+            <param argument="--pseudo" type="boolean" truevalue="--pseudo" falsevalue="" label="Correct erroneously labeled pseudogenes"/>   
         </section>
         <section name="output_options" title="Output options" expanded="false">
-            <param argument="--retainids" type="boolean"
-                truevalue="--retainids" falsevalue=""
-                label="Retain original feature IDs"
-                help="Retain original feature IDs from input files; conflicts will arise if input contains duplicated ID values"/>
-            <param argument="--namefmt" type="text"
-                value="" optional="true"
-                label="ID format for newly created locy"
-                help="Provide a format string to override the default ID format for newly created loci; default is &quot;locus%lu&quot; (locus1, locus2, etc) for loci and &quot;iLocus%lu&quot; (iLocus1, iLocus2, etc) for interval loci; note the format string should include a single %lu specifier to be filled in with a long unsigned integer value."/>
-            <param name="outputfiles" type="select" display="checkboxes" label="Output files"
-                multiple="true" optional="true" >
+            <param argument="--retainids" type="boolean" truevalue="--retainids" falsevalue="" label="Retain original feature IDs" help="Retain original feature IDs from input files; conflicts will arise if input contains duplicated ID values"/>
+            <param argument="--namefmt" type="text" value="" optional="true" label="ID format for newly created locy" help="Provide a format string to override the default ID format for newly created loci; default is &quot;locus%lu&quot; (locus1, locus2, etc) for loci and &quot;iLocus%lu&quot; (iLocus1, iLocus2, etc) for interval loci; note the format string should include a single %lu specifier to be filled in with a long unsigned integer value."/>
+            <param name="outputfiles" type="select" display="checkboxes" label="Output files" multiple="true" optional="true" >
                 <option value="ilens">Create file with the lenghts of each intergenic iLocus</option>
                 <option value="genemap">Create a mapping from each gene annotation to its correspondig locus</option>
                 <option value="transmap">Create a mapping from each transcript annotation to its correspondent locus</option>
@@ -109,7 +81,7 @@
 
     </inputs>
     <outputs>
-        <data name="output" format="tabular" />
+        <data name="output" format="tabular"/>
         <data name="output_ilens" format="tabular" label="${tool.name} on ${on_string}: Intergenic regions lengths">
             <filter>output_options["outputfiles"] and "ilens" in output_options["outputfiles"]</filter>
         </data>
@@ -181,8 +153,10 @@
         <test expect_num_outputs="4">
             <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
 	        <section name="refine_options">
-                <param name="refine_parameters|refine" value="--refine"/>
-                <param name="refine_options|minoverlap" value="5"/>
+                <conditional name="refine_parameters">
+                    <param name="refine" value="--refine"/>
+                </conditional>
+                <param name="minoverlap" value="5"/>
 	        </section>
             <section name="ilocus_parsing">
                 <param name="delta" value="400"/>
diff --git a/tools/aegean/macros.xml b/tools/aegean/macros.xml
index 2977595e675..334e82a546b 100644
--- a/tools/aegean/macros.xml
+++ b/tools/aegean/macros.xml
@@ -33,4 +33,5 @@
     </xml>
     <token name="@TOOL_VERSION@">0.16.0</token>
     <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">20.01</token>
 </macros>   
diff --git a/tools/aegean/parseval.xml b/tools/aegean/parseval.xml
index b9f9913240d..f841595bb46 100644
--- a/tools/aegean/parseval.xml
+++ b/tools/aegean/parseval.xml
@@ -1,4 +1,4 @@
-<tool id="aegean_parseval" name="AEGeAn ParsEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+<tool id="aegean_parseval" name="AEGeAn ParsEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description> compare two sets of gene annotations for the same sequence.</description>
     <macros>                                                                                           
         <import>macros.xml</import>
@@ -36,25 +36,14 @@
     <inputs>
         <param name="referencegff3" type="data"  format="gff3" label="Reference GFF3 file"/>
         <param name="predictiongff3" type="data"  format="gff3" label="Prediction GFF3 file"/>
-        <param argument="--delta" type="integer"
-            min="0" max="20" value="0" 
-            label="Number of nucleotides to extend gene loci"/>
-        <param argument="--maxtrans" type="integer" 
-            min="1" max="50" value="32"
-            label="Maximum transcript allowed per locus" />
-        <param name="output_type" type="select"
-            label="Select the output type">
+        <param argument="--delta" type="integer" min="0" max="20" value="0" label="Number of nucleotides to extend gene loci"/>
+        <param argument="--maxtrans" type="integer" min="1" max="50" value="32" label="Maximum transcript allowed per locus" />
+        <param name="output_type" type="select" label="Select the output type">
             <option value="text">Text</option>
             <option value="html">HTML</option>
         </param>
-        <param argument="--refrlabel" type="text"
-            value="" optional="true"
-            label="Reference annotations"
-            help="Optional label for reference annotations"/>
-        <param argument="--predlabel" type="text"
-            value="" optional="true"
-            label="Prediction annotations"
-            help="Optional label for prediction annotations"/>
+        <param argument="--refrlabel" type="text" value="" optional="true" label="Reference annotations" help="Optional label for reference annotations"/>
+        <param argument="--predlabel" type="text" value="" optional="true" label="Prediction annotations" help="Optional label for prediction annotations"/>
     </inputs>
     <outputs>
         <data name="output_txt" format="txt" label="${tool.name} on ${on_string}: text">
diff --git a/tools/aldex2/.lint_skip b/tools/aldex2/.lint_skip
deleted file mode 100644
index 2092d1d0d68..00000000000
--- a/tools/aldex2/.lint_skip
+++ /dev/null
@@ -1 +0,0 @@
-TestsCaseValidation
diff --git a/tools/aldex2/aldex2.xml b/tools/aldex2/aldex2.xml
index 1eb92da7602..218c7f06699 100644
--- a/tools/aldex2/aldex2.xml
+++ b/tools/aldex2/aldex2.xml
@@ -244,9 +244,11 @@ Rscript '${__tool_directory__}/aldex2.R'
                 <param name="group_name" value="S"/>
                 <param name="num_cols" value="7"/>
             </repeat>
-            <param name="effect" value="false"/>
-            <param name="include_sample_summary" value="true"/>
-            <param name="iterate" value="true"/>
+            <conditional name="analysis_type_cond">
+                <param name="effect" value="false"/>
+                <param name="include_sample_summary" value="true"/>
+                <param name="iterate" value="true"/>
+            </conditional>
             <output name="output_aldex" ftype="tabular">
                 <assert_contents>
                     <has_text text="we.ep"/>
@@ -264,7 +266,9 @@ Rscript '${__tool_directory__}/aldex2.R'
                 <param name="group_name" value="S"/>
                 <param name="num_cols" value="7"/>
             </repeat>
-            <param name="aldex_test" value="kw"/>
+            <conditional name="analysis_type_cond">
+                <param name="aldex_test" value="kw"/>
+            </conditional>
             <output name="output_aldex" ftype="tabular">
                 <assert_contents>
                     <has_text text="kw.ep"/>
@@ -282,15 +286,17 @@ Rscript '${__tool_directory__}/aldex2.R'
                 <param name="group_name" value="S"/>
                 <param name="num_cols" value="7"/>
             </repeat>
-            <param name="analysis_type" value="aldex_corr"/>
-            <repeat name="cont_var">
-                <param name="group_num" value="1"/>
-                <param name="num_cols_in_group" value="7"/>
-            </repeat>
-            <repeat name="cont_var">
-                <param name="group_num" value="2"/>
-                <param name="num_cols_in_group" value="7"/>
-            </repeat>
+            <conditional name="analysis_type_cond">
+                <param name="analysis_type" value="aldex_corr"/>
+                <repeat name="cont_var">
+                    <param name="group_num" value="1"/>
+                    <param name="num_cols_in_group" value="7"/>
+                </repeat>
+                <repeat name="cont_var">
+                    <param name="group_num" value="2"/>
+                    <param name="num_cols_in_group" value="7"/>
+                </repeat>
+            </conditional>
             <output name="output_aldex_corr" ftype="tabular">
                 <assert_contents>
                     <has_text text="pearson.ecor"/>
@@ -308,7 +314,9 @@ Rscript '${__tool_directory__}/aldex2.R'
                 <param name="group_name" value="S"/>
                 <param name="num_cols" value="7"/>
             </repeat>
-            <param name="analysis_type" value="aldex_effect"/>
+            <conditional name="analysis_type_cond">
+                <param name="analysis_type" value="aldex_effect"/>
+            </conditional>
             <output name="output_aldex_effect" ftype="tabular">
                 <assert_contents>
                     <has_text text="rab.all"/>
@@ -326,7 +334,9 @@ Rscript '${__tool_directory__}/aldex2.R'
                 <param name="group_name" value="S"/>
                 <param name="num_cols" value="7"/>
             </repeat>
-            <param name="analysis_type" value="aldex_expected_distance"/>
+            <conditional name="analysis_type_cond">
+                <param name="analysis_type" value="aldex_expected_distance"/>
+            </conditional>
             <output name="output_aldex_expected_distance" ftype="png">
                 <assert_contents>
                     <has_size value="70183" delta="4000"/>
@@ -343,7 +353,9 @@ Rscript '${__tool_directory__}/aldex2.R'
                 <param name="group_name" value="S"/>
                 <param name="num_cols" value="7"/>
             </repeat>
-            <param name="analysis_type" value="aldex_kw"/>
+            <conditional name="analysis_type_cond">
+                <param name="analysis_type" value="aldex_kw"/>
+            </conditional>
             <output name="output_aldex_kw" ftype="tabular">
                 <assert_contents>
                     <has_text text="kw.ep"/>
@@ -361,7 +373,9 @@ Rscript '${__tool_directory__}/aldex2.R'
                 <param name="group_name" value="S"/>
                 <param name="num_cols" value="7"/>
             </repeat>
-            <param name="analysis_type" value="aldex_plot"/>
+            <conditional name="analysis_type_cond">
+                <param name="analysis_type" value="aldex_plot"/>
+            </conditional>
             <output name="output_aldex_plot" ftype="png">
                 <assert_contents>
                     <has_size value="19064" delta="500"/>
@@ -378,8 +392,10 @@ Rscript '${__tool_directory__}/aldex2.R'
                 <param name="group_name" value="S"/>
                 <param name="num_cols" value="7"/>
             </repeat>
-            <param name="analysis_type" value="aldex_plot_feature"/>
-            <param name="feature_name" value="A:D:A:E"/>
+            <conditional name="analysis_type_cond">
+                <param name="analysis_type" value="aldex_plot_feature"/>
+                <param name="feature_name" value="A:D:A:E"/>
+            </conditional>
             <output name="output_aldex_plot_feature" ftype="png">
                 <assert_contents>
                     <has_size value="30772" delta="2000"/>
@@ -396,7 +412,9 @@ Rscript '${__tool_directory__}/aldex2.R'
                 <param name="group_name" value="S"/>
                 <param name="num_cols" value="7"/>
             </repeat>
-            <param name="analysis_type" value="aldex_ttest"/>
+            <conditional name="analysis_type_cond">
+                <param name="analysis_type" value="aldex_ttest"/>
+            </conditional>
             <output name="output_aldex_ttest" ftype="tabular">
                 <assert_contents>
                     <has_text text="we.ep"/>
@@ -414,9 +432,11 @@ Rscript '${__tool_directory__}/aldex2.R'
                 <param name="group_name" value="S"/>
                 <param name="num_cols" value="7"/>
             </repeat>
-            <param name="analysis_type" value="aldex_ttest"/>
-            <param name="paired_test" value="true"/>
-            <param name="hist_plot" value="true"/>
+            <conditional name="analysis_type_cond">
+                <param name="analysis_type" value="aldex_ttest"/>
+                <param name="paired_test" value="true"/>
+                <param name="hist_plot" value="true"/>
+            </conditional>
             <output name="output_aldex_ttest" ftype="tabular">
                 <assert_contents>
                     <has_text text="we.ep"/>