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[WIP] Remove .lint_skip files (1) #7892

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91a905f
Remove .lint_skip files from adapter_removal
SaimMomin12 Apr 14, 2026
0a77ca2
Remove .lint_skip files from aegean
SaimMomin12 Apr 14, 2026
8a7d536
Remove .lint_skip files from aldex2
SaimMomin12 Apr 14, 2026
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1 change: 0 additions & 1 deletion tools/adapter_removal/.lint_skip
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56 changes: 33 additions & 23 deletions tools/adapter_removal/adapter_removal.xml
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Expand Up @@ -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"/>
Expand All @@ -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"/>
Expand Down Expand Up @@ -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"/>
Expand All @@ -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"/>
Expand All @@ -355,11 +363,13 @@ $fastq_merging_options.collapse_conservatively
</assert_contents>
</output>
</test>
<!-- Dataset pair input, all defaults, all optional outputs checked -->
<!-- Test 05: Dataset pair input, all defaults, all optional outputs checked -->
<test expect_num_outputs="7">
<param name="input_type" value="pair"/>
<param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
<param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
<conditional name="input_type_cond">
<param name="input_type" value="pair"/>
<param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
<param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
</conditional>
<param name="output_select" value="output_singleton,output_collapsed,output_collapsed_truncated,output_discarded"/>
<output name="output_settings" ftype="txt">
<assert_contents>
Expand Down
2 changes: 0 additions & 2 deletions tools/aegean/.lint_skip
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55 changes: 16 additions & 39 deletions tools/aegean/gaeval.xml
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@@ -1,5 +1,5 @@
<tool id="aegean_gaeval" name="AEGeAn GAEVAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
<description> compute coverage and integrity scores for gene models using transcript alignments.</description>
<tool id="aegean_gaeval" name="AEGeAn GAEVAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description> compute coverage and integrity scores for gene models using transcript alignments</description>
<macros>
<import>macros.xml</import>
</macros>
Expand All @@ -9,57 +9,35 @@
<version_command>gaeval --version</version_command>
<command detect_errors="exit_code">
<![CDATA[
gaeval "$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">
Expand All @@ -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>
Expand All @@ -88,7 +66,6 @@
</section>
<output name="output" file="gaeval_output_test3.txt" lines_diff="2"/>
</test>

</tests>
<help>
<![CDATA[
Expand Down
62 changes: 18 additions & 44 deletions tools/aegean/locuspocus.xml
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@@ -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>
Expand Down Expand Up @@ -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>
Expand All @@ -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>
Expand Down Expand Up @@ -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"/>
Expand Down
1 change: 1 addition & 0 deletions tools/aegean/macros.xml
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Expand Up @@ -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>
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