Update metaQuantome tools to version 2.0.4 (#823)

reid-wagner · web-flow · commit 6bdf8fc7f19e · 2026-05-08T14:35:32.000-05:00
* Update metaQuantome to version 2.0.4. Remove unused --slim_down parameter from filter and stat modules. Add new --load_obsolete feature to allow expand module to load obsolete GO terms from database.

* Updates for linting: Add profile. Fix test parameter definitions. Remove unnecessary 'name' attribute from 'unique_value' filters.

* Update test outputs.
diff --git a/tools/metaquantome/macros.xml b/tools/metaquantome/macros.xml
@@ -1,6 +1,7 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.0.2</token>
+    <token name="@TOOL_VERSION@">2.0.4</token>
     <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">25.0</token>
     <xml name="xrefs">
         <xrefs>
             <xref type="bio.tools">metaQuantome</xref>
@@ -15,35 +16,13 @@
     <xml name="db">
         <param argument="db_tar" type="data" label="Database Archive File"/>
     </xml>
-    <xml name="ONTOLOGY_ARGS">
-        <conditional name="ontology_args">
-            <param name="ontology" type="select" label="Ontology">
-                <option value="go">Gene Ontology (GO terms)</option>
-                <option value="ec">Enzyme Commission (EC) numbers</option>
-                <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
-            </param>
-            <when value="go">
-                <param argument="--slim_down" type="boolean" label="Use slim GO"/>
-            </when>
-            <when value="ec">
-                <!-- do nothing -->
-            </when>
-            <when value="cog">
-                <!-- do nothing -->
-            </when>
-        </conditional>
+    <xml name="ONTOLOGY_SELECT">
+        <param name="ontology" type="select" label="Ontology">
+            <option value="go">Gene Ontology (GO terms)</option>
+            <option value="ec">Enzyme Commission (EC) numbers</option>
+            <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
+        </param>
     </xml>
-    <token name="@COMMON_PARAMS@"><![CDATA[
-            --samps '$samps'
-            --mode '$mode_args.mode'
-            #if $mode_args.mode == 'f'
-                --ontology='$mode_args.ontology_args.ontology'
-            #end if
-            #if $mode_args.mode == 'ft'
-                --ontology='$mode_args.ontology_args.ontology'
-            #end if
-    ]]>
-    </token>
     <xml name="SAMPS">
         <param name="samps" type="data" format="tabular" label="Samples file" help="must be created by 'metaQuantome: create samples file'"/>
     </xml>
diff --git a/tools/metaquantome/metaquantome_db.xml b/tools/metaquantome/metaquantome_db.xml
@@ -1,4 +1,4 @@
-<tool id="metaquantome_db" name="metaQuantome: database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="metaquantome_db" name="metaQuantome: database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>download the GO, EC, and NCBI databases</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/metaquantome/metaquantome_expand.xml b/tools/metaquantome/metaquantome_expand.xml
@@ -1,4 +1,4 @@
-<tool id="metaquantome_expand" name="metaQuantome: expand" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="metaquantome_expand" name="metaQuantome: expand" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>a set of functional or taxonomy annotations</description>
     <macros>
         <import>macros.xml</import>
@@ -41,6 +41,22 @@
                 <option value="kingdom">kingdom</option>
             </param>
         </xml>
+        <xml name="ONTOLOGY_CONDITIONAL">
+            <conditional name="ontology_conditional">
+                <expand macro="ONTOLOGY_SELECT"/>
+                <when value="go">
+                    <param argument="--slim_down" type="boolean" label="Use slim GO"/>
+                    <param argument="--load_obsolete" type="boolean" label="Load obsolete GO terms from the database"/>
+                </when>
+                <when value="ec">
+                    <!-- do nothing -->
+                </when>
+                <when value="cog">
+                    <!-- do nothing -->
+                </when>
+            </conditional>
+        </xml>
+
         <token name="@FUNC_FILE@">
       --func_file='$mode_args.func_file'
       --pep_colname_func='$mode_args.pep_colname_func'
@@ -49,11 +65,14 @@
       --func_colname='$mode_args.func_colname'
     </token>
         <token name="@ONTOLOGY@">
-      --ontology='$mode_args.ontology_args.ontology'
-      #if $mode_args.ontology_args.ontology == 'go'
-          #if $mode_args.ontology_args.slim_down
+      --ontology='$mode_args.ontology_conditional.ontology'
+      #if $mode_args.ontology_conditional.ontology == 'go'
+          #if $mode_args.ontology_conditional.slim_down
               --slim_down
           #end if
+          #if $mode_args.ontology_conditional.load_obsolete
+              --load_obsolete
+          #end if
       #end if
     </token>
         <token name="@TAX_FILE@">
@@ -105,7 +124,7 @@
             </param>
             <when value="f">
                 <expand macro="FUNC_FILE"/>
-                <expand macro="ONTOLOGY_ARGS"/>
+                <expand macro="ONTOLOGY_CONDITIONAL"/>
                 <expand macro="FUNC_COLNAME"/>
             </when>
             <when value="t">
@@ -115,7 +134,7 @@
             <when value="ft">
                 <expand macro="FUNC_FILE"/>
                 <expand macro="FUNC_COLNAME"/>
-                <expand macro="ONTOLOGY_ARGS"/>
+                <expand macro="ONTOLOGY_CONDITIONAL"/>
                 <expand macro="TAX_FILE"/>
                 <expand macro="TAX_COLNAME"/>
                 <expand macro="FT_TAR_RANK"/>
@@ -135,11 +154,11 @@
             <param name="samps" value="samples_basic.tab" ftype="tabular"/>
             <param name="int_file" value="int_ttest.tab" ftype="tabular"/>
             <param name="pep_colname_int" value="peptide"/>
-            <param name="func_file" value="multiple_func.tab"/>
-            <param name="pep_colname_func" value="peptide"/>
-            <param name="func_colname" value="ec"/>
-            <param name="mode" value="f"/>
-            <param name="ontology" value="ec"/>
+            <param name="mode_args|func_file" value="multiple_func.tab"/>
+            <param name="mode_args|pep_colname_func" value="peptide"/>
+            <param name="mode_args|func_colname" value="ec"/>
+            <param name="mode_args|mode" value="f"/>
+            <param name="mode_args|ontology_conditional|ontology" value="ec"/>
             <output name="outfile">
                 <assert_contents>
                     <has_text text="1.2.7.10"/>
diff --git a/tools/metaquantome/metaquantome_filter.xml b/tools/metaquantome/metaquantome_filter.xml
@@ -1,4 +1,4 @@
-<tool id="metaquantome_filter" name="metaQuantome: filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="metaquantome_filter" name="metaQuantome: filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>for quality, redundancy, and sample coverage</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,7 @@
         --samps '$samps'
         --mode '$mode_args.mode'
         #if $mode_args.mode == 'f' or $mode_args.mode == 'ft'
-            --ontology='$mode_args.ontology_args.ontology'
+            --ontology='$mode_args.ontology'
         #end if
         --expand_file '$expand_file'
         --min_peptides $min_peptides
@@ -36,12 +36,12 @@
               <option value="ft">Functional-taxonomic interaction analysis</option>
           </param>
           <when value="f">
-              <expand macro="ONTOLOGY_ARGS"/>
+              <expand macro="ONTOLOGY_SELECT"/>
           </when>
           <when value="t">
           </when>
           <when value="ft">
-              <expand macro="ONTOLOGY_ARGS"/>
+              <expand macro="ONTOLOGY_SELECT"/>
           </when>
       </conditional>
       <expand macro="SAMPS"/>
@@ -58,7 +58,7 @@
               The default is 0.
           </help>
       </param>
-      <param argument="--min_pep_nsamp" type="integer" value="" min="0" optional="true" label="min_pep_nsamp">
+      <param argument="--min_pep_nsamp" type="integer" min="0" optional="true" label="min_pep_nsamp">
           <help>
               Number of samples per group that must meet or exceed
               min_peptides. Default is 'all'.
@@ -71,7 +71,7 @@
               than or equal to min_children_non_leaf. The default is 0.
           </help>
       </param>
-      <param argument="--min_child_nsamp" type="integer" value="" min="0" optional="true" label="min_child_nsamp">
+      <param argument="--min_child_nsamp" type="integer" min="0" optional="true" label="min_child_nsamp">
           <help>
               Number of samples per group that must meet or exceed
               min_children_nsamp. The default is all samples.
@@ -93,13 +93,11 @@
     <tests>
       <test>
         <param name="expand_file" value="go_expanded.tab" ftype="tabular"/>
-        <param name="mode" value="f" />
-        <param name="ontology" value="go" />
+        <param name="mode_args|mode" value="f" />
+        <param name="mode_args|ontology" value="go" />
         <param name="samps" value="samples_basic.tab" ftype="tabular"/>
         <param name="min_peptides" value="2" />
-        <param name="min_pep_nsamp" value="" />
         <param name="min_children_non_leaf" value="2" />
-        <param name="min_child_nsamp" value="" />
         <param name="qthreshold" value="0" />
         <output name="outfile" file="go_filtered.tab" ftype="tabular"/>
       </test>
diff --git a/tools/metaquantome/metaquantome_sample.xml b/tools/metaquantome/metaquantome_sample.xml
@@ -1,4 +1,4 @@
-<tool id="metaquantome_sample" name="metaQuantome: create samples file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="metaquantome_sample" name="metaQuantome: create samples file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description> by specifying the experiment's groups and associated column names</description>
     <macros>
         <import>macros.xml</import>
@@ -47,25 +47,25 @@
     </outputs>
     <tests>
         <test>
-            <param name="samps_src" value="build" />
-            <repeat name="samps">
+            <param name="samps_args|samps_src" value="build" />
+            <repeat name="samps_args|samps">
                 <param name="group_name" value="NS"/>
                 <param name="col_names" value="X737NS,X852NS,X867NS"/>
             </repeat>
-            <repeat name="samps">
+            <repeat name="samps_args|samps">
                 <param name="group_name" value="WS"/>
                 <param name="col_names" value="X737WS,X852WS,X867WS"/>
             </repeat>
             <output name="samples_file" file="samples.tab" ftype="tabular"/>
         </test>
         <test>
-            <param name="samps_src" value="history" />
-            <param name="file" value="int_737_test.tab" ftype="tabular" />
-            <repeat name="samps">
+            <param name="samps_args|samps_src" value="history" />
+            <param name="samps_args|file" value="int_737_test.tab" ftype="tabular" />
+            <repeat name="samps_args|samps">
                 <param name="group_name" value="NS"/>
                 <param name="col_names" value="3,5,7"/>
             </repeat>
-            <repeat name="samps">
+            <repeat name="samps_args|samps">
                 <param name="group_name" value="WS"/>
                 <param name="col_names" value="2,4,6"/>
             </repeat>
diff --git a/tools/metaquantome/metaquantome_stat.xml b/tools/metaquantome/metaquantome_stat.xml
@@ -1,4 +1,4 @@
-<tool id="metaquantome_stat" name="metaQuantome: stat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="metaquantome_stat" name="metaQuantome: stat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>differential analysis of functional expression and taxonomic abundance</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,7 @@
         --samps '$samps'
         --mode '$mode_args.mode'
         #if $mode_args.mode == 'f' or $mode_args.mode == 'ft'
-            --ontology='$mode_args.ontology_args.ontology'
+            --ontology='$mode_args.ontology'
         #end if
         --file '$file'
         --control_group '$control_group'
@@ -29,12 +29,12 @@
                 <option value="ft">Functional-taxonomic interaction analysis</option>
             </param>
             <when value="f">
-                <expand macro="ONTOLOGY_ARGS"/>
+                <expand macro="ONTOLOGY_SELECT"/>
             </when>
             <when value="t">
             </when>
             <when value="ft">
-                <expand macro="ONTOLOGY_ARGS"/>
+                <expand macro="ONTOLOGY_SELECT"/>
             </when>
         </conditional>
         <param argument="--control_group" type="text" label="Name of the control sample group of control (used as denominator for fold change evaluation).">
@@ -53,8 +53,8 @@
       <test>
         <param name="file" value="ec_ttest.tab" ftype="tabular" />
         <param name="parametric" value="True" />
-        <param name="ontology" value="ec" />
-        <param name="mode" value="f" />
+        <param name="mode_args|ontology" value="ec" />
+        <param name="mode_args|mode" value="f" />
         <param name="samps" value="samples_basic.tab" ftype="tabular" />
         <param name="control_group" value="s2"/>
         <output name="outfile" value="ec_ttest_tested.tab" ftype="tabular"/>
diff --git a/tools/metaquantome/metaquantome_viz.xml b/tools/metaquantome/metaquantome_viz.xml
diff --git a/tools/metaquantome/test-data/ec_ttest_tested.tab b/tools/metaquantome/test-data/ec_ttest_tested.tab
diff --git a/tools/metaquantome/test-data/go_filtered.tab b/tools/metaquantome/test-data/go_filtered.tab

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="metaquantome_db" name="metaQuantome: database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">`
	`1`	`+<tool id="metaquantome_db" name="metaQuantome: database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">`
`2`	`2`	`<description>download the GO, EC, and NCBI databases</description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`