Merge pull request #6417 from bernt-matthias/lint-colibread

Linter fixes colibread
galaxyproject · Oct 5, 2024 · 747394d · 747394d
2 parents c36c44c + af59f06
commit 747394d
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diff --git a/tools/colibread/.lint_skip b/tools/colibread/.lint_skip
diff --git a/tools/colibread/commet.xml b/tools/colibread/commet.xml
@@ -1,10 +1,11 @@
-<tool id="commet" name="Commet" version="24.7.14+galaxy0" profile="@PROFILE@">
+<tool id="commet" name="Commet" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>COmpare Multiple METagenomes</description>
     <macros>
+        <token name="@TOOL_VERSION@">24.7.14</token>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="24.7.14">commet</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">commet</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #for $i, $set in enumerate($sets):
@@ -45,29 +46,28 @@
         <param name="percentage_outputs" label="Generate percentage files" type="boolean" checked="false"/>
     </inputs>
     <outputs>
-        <data format="csv" name="matrix_plain" from_work_dir="output_commet/matrix_plain.csv" label="Matrix plain with ${tool.name} on ${on_string}" >
+        <data format="csv" name="matrix_plain" from_work_dir="output_commet/matrix_plain.csv" label="${tool.name} on ${on_string}: Matrix plain" >
             <filter>plain_outputs</filter>
         </data>
-        <data format="csv" name="matrix_percentage" from_work_dir="output_commet/matrix_percentage.csv" label="Matrix percentage with ${tool.name} on ${on_string}" >
+        <data format="csv" name="matrix_percentage" from_work_dir="output_commet/matrix_percentage.csv" label="${tool.name} on ${on_string}: Matrix percentage" >
             <filter>percentage_outputs</filter>
         </data>
-        <data format="csv" name="matrix_normalized" from_work_dir="output_commet/matrix_normalized.csv" label="Matrix normalized with ${tool.name} on ${on_string}" >
+        <data format="csv" name="matrix_normalized" from_work_dir="output_commet/matrix_normalized.csv" label="${tool.name} on ${on_string}: Matrix normalized" >
             <filter>normalized_outputs</filter>
         </data>
-        <data format="png" name="dendrogram_normalized" from_work_dir="output_commet/dendrogram_normalized.png" label="Dendrogram ${tool.name} on ${on_string}" />
-        <data format="png" name="heatmap_normalized" from_work_dir="output_commet/heatmap_normalized.png" label="Heatmap normalized with ${tool.name} on ${on_string}" >
+        <data format="png" name="dendrogram_normalized" from_work_dir="output_commet/dendrogram_normalized.png" label="${tool.name} on ${on_string}: Dendrogram" />
+        <data format="png" name="heatmap_normalized" from_work_dir="output_commet/heatmap_normalized.png" label="${tool.name} on ${on_string}: Heatmap normalized" >
             <filter>normalized_outputs</filter>
         </data>
-        <data format="png" name="heatmap_percentage" from_work_dir="output_commet/heatmap_percentage.png" label="Heatmap percentage with ${tool.name} on ${on_string}" >
+        <data format="png" name="heatmap_percentage" from_work_dir="output_commet/heatmap_percentage.png" label="${tool.name} on ${on_string}: Heatmap percentage" >
             <filter>percentage_outputs</filter>
         </data>
-        <data format="png" name="heatmap_plain" from_work_dir="output_commet/heatmap_plain.png" label="Heatmap Plain with ${tool.name} on ${on_string}" >
+        <data format="png" name="heatmap_plain" from_work_dir="output_commet/heatmap_plain.png" label="${tool.name} on ${on_string}: Heatmap Plain" >
             <filter>plain_outputs</filter>
         </data>
     </outputs>
     <tests>
-        <test>
-            <param name="input_type" value="list" />
+        <test expect_num_outputs="5">
             <repeat name="sets">
                 <param name="reads" value="commet/A.fa.gz" ftype="fasta.gz" />
             </repeat>
@@ -80,6 +80,11 @@
             <param name="plain_outputs" value="True"/>
             <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/>
             <output name="matrix_plain" file="commet/matrix_plain.csv"/>
+            <output name="heatmap_plain">
+                <assert_contents>
+                    <has_size size="1k"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/colibread/discosnp_RAD.xml b/tools/colibread/discosnp_RAD.xml
@@ -1,6 +1,7 @@
-<tool id="discosnp_rad" name="DiscoSnpRAD" version="@DISCOSNP_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="discosnp_rad" name="DiscoSnpRAD" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>discovering polymorphism from raw unassembled RADSeq NGS reads.</description>
     <macros>
+        <token name="@TOOL_VERSION@">2.5.4</token>
         <import>macros.xml</import>
     </macros>
     <expand macro="discosnp_requirements" />
@@ -43,8 +44,8 @@
       <expand macro="discosnp_options" />
   </inputs>
   <outputs>
-      <data name="vcf" from_work_dir="discoRad_*_clustered.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
-      <data name="fasta" from_work_dir="discoRad_*_raw.fa" format="fasta" label="Fasta with ${tool.name} on $on_string"/>
+      <data name="vcf" from_work_dir="discoRad_*_clustered.vcf" format="vcf" label="${tool.name} on ${on_string}: VCF"/>
+      <data name="fasta" from_work_dir="discoRad_*_raw.fa" format="fasta" label="${tool.name} on ${on_string}: FASTA"/>
   </outputs>
   <tests>
       <test>
@@ -55,7 +56,6 @@
           <param name="D" value="0"/>
           <param name="P" value="4"/>
           <param name="k" value="31"/>
-          <param name="b" value="2"/>
           <param name="max_size_cluster" value="50"/>
           <param name="max_missing" value="0.95"/>
           <param name="min_rank" value="0.0"/>

diff --git a/tools/colibread/discosnp_pp.xml b/tools/colibread/discosnp_pp.xml
@@ -1,6 +1,7 @@
-<tool id="discosnp_pp" name="DiscoSnp++" version="@DISCOSNP_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="discosnp_pp" name="DiscoSnp++" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>is an efficient tool for detecting SNPs without a reference genome.</description>
     <macros>
+        <token name="@TOOL_VERSION@">2.5.4</token>
         <import>macros.xml</import>
     </macros>
     <expand macro="discosnp_requirements" />
@@ -57,8 +58,8 @@
       </conditional>
   </inputs>
   <outputs>
-      <data name="vcf" from_work_dir="*_coherent.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
-      <data name="fasta" from_work_dir="*_coherent.fa" format="fasta" label="Multifasta with ${tool.name} on $on_string"/>
+      <data name="vcf" from_work_dir="*_coherent.vcf" format="vcf" label="${tool.name} on ${on_string}: VCF"/>
+      <data name="fasta" from_work_dir="*_coherent.fa" format="fasta" label="${tool.name} on ${on_string}: FASTA"/>
   </outputs>
   <tests>
       <test>

diff --git a/tools/colibread/kissplice.xml b/tools/colibread/kissplice.xml
@@ -1,4 +1,4 @@
-<tool id="kissplice" name="KisSplice" version="2.4.0+galaxy0" profile="@PROFILE@">
+<tool id="kissplice" name="KisSplice" version="2.4.0+galaxy1" profile="@PROFILE@">
     <description>is a local transcriptome assembler for SNPs, indels and AS events</description>
     <macros>
         <import>macros.xml</import>
@@ -26,7 +26,7 @@
         <param argument="-k" type="integer" value="41" label="K-mer length" />
         <param argument="-c" type="integer" value="2" label="K-mers present strictly less than this number of times in the dataset will be discarded (integer value required)" />
         <param argument="-C" type="float" value="0.05" label="Edges with relative coverage below this number are removed (value in [0,1) required)" />
-        <param name="output_context" argument="--output-context" type="boolean" checked="false" truevalue="--output-context" falsevalue="" label="Output the maximum non-ambiguous context of each event" />
+        <param argument="--output-context" type="boolean" checked="false" truevalue="--output-context" falsevalue="" label="Output the maximum non-ambiguous context of each event" />
         <param argument="--counts" type="select" label="Selecting how the counts will be reported">
             <option value="0">Total counts</option>
             <option value="1">Counts on junctions</option>
@@ -38,30 +38,61 @@
         </param>
     </inputs>
     <outputs>
-        <data name="type0a" format="fasta" label="Single SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0a.fa">
+        <data name="type0a" format="fasta" label="${tool.name} on ${on_string}: Single SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0a.fa">
             <filter>output_option == 'all_files'</filter>
         </data>
-        <data name="type0b" format="fasta" label="Multiple SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0b.fa">
+        <data name="type0b" format="fasta" label="${tool.name} on ${on_string}: Multiple SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0b.fa">
             <filter>output_option == 'all_files'</filter>
         </data>
-        <data name="type1" format="fasta" label="Alternative splicing events" from_work_dir="results/*_coherents_type_1.fa"/>
-        <data name="type2" format="fasta" label="Inexact tandem repeats" from_work_dir="results/*_coherents_type_2.fa">
+        <data name="type1" format="fasta" label="${tool.name} on ${on_string}: Alternative splicing events" from_work_dir="results/*_coherents_type_1.fa"/>
+        <data name="type2" format="fasta" label="${tool.name} on ${on_string}: Inexact tandem repeats" from_work_dir="results/*_coherents_type_2.fa">
             <filter>output_option == 'all_files'</filter>
         </data>
-        <data name="type3" format="fasta" label="Short indels" from_work_dir="results/*_coherents_type_3.fa">
+        <data name="type3" format="fasta" label="${tool.name} on ${on_string}: Short indels" from_work_dir="results/*_coherents_type_3.fa">
             <filter>output_option == 'all_files'</filter>
         </data>
-        <data name="type4" format="fasta" label="Other events" from_work_dir="results/*_coherents_type_4.fa">
+        <data name="type4" format="fasta" label="${tool.name} on ${on_string}: Other events" from_work_dir="results/*_coherents_type_4.fa">
             <filter>output_option == 'all_files'</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" />
             <param name="k" value="25"/>
             <param name="output_option" value="alternative_file" />
             <output name="type1" file="kissplice/alternative_splicing.fa"/>
         </test>
+        <test expect_num_outputs="6">
+            <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" />
+            <param name="k" value="25"/>
+            <param name="output_option" value="all_files" />
+            <output name="type0a">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+            <output name="type0b">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+            <output name="type1" file="kissplice/alternative_splicing.fa"/>
+            <output name="type2">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+            <output name="type3">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+            <output name="type4">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 
@@ -82,17 +113,7 @@ References, documentation and FAQ here_.
 
     ]]></help>
     <expand macro="citations">
-        <citation type="bibtex">
-         @article{PMID:22537044,
-          author       = {Sacomoto, G. A. and Kielbassa, J. and Chikhi, R. and Uricaru, R. and Antoniou, P. and Sagot, M. F. and Peterlongo, P. and Lacroix, V.},
-          title        = {KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.},
-          journal      = {BMC Bioinformatics},
-          year         = {2012},
-          volume       = {13 Suppl 6},
-          pages        = {S5},
-          url          = {http://www.ncbi.nlm.nih.gov/pubmed/22537044},
-        }
-        </citation>
+        <citation type="doi">10.1186/1471-2105-13-S6-S5</citation>
     </expand>
 
 </tool>
diff --git a/tools/colibread/lordec.xml b/tools/colibread/lordec.xml
@@ -1,10 +1,11 @@
-<tool id="lordec" name="Lordec" version="0.9+galaxy2" profile="@PROFILE@">
+<tool id="lordec" name="Lordec" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
     <description>is a set a programs for correcting sequencing errors in PacBio reads</description>
     <macros>
+        <token name="@TOOL_VERSION@">0.9</token>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.9">lordec</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">lordec</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if str( $program_type_choice.program_type ) == "correct":
@@ -63,18 +64,18 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="fasta" name="corrected_read_file" label="Corrected long reads with ${tool.name} on ${on_string}" >
+        <data format="fasta" name="corrected_read_file" label="${tool.name} on ${on_string}: Corrected long reads" >
             <filter>program_type_choice['program_type'] == 'correct'</filter>
         </data>
-        <data format="fasta" name="trimmed_reads_file" label="Trimmed reads file with ${tool.name} on ${on_string}" >
+        <data format="fasta" name="trimmed_reads_file" label="${tool.name} on ${on_string}: Trimmed reads" >
             <filter>program_type_choice['program_type'] == 'trim'</filter>
         </data>
-        <data format="tabular" name="stat_file" label="Stats with ${tool.name} on ${on_string}" >
+        <data format="tabular" name="stat_file" label="${tool.name} on ${on_string}: Stats" >
             <filter>program_type_choice['program_type'] == 'stats'</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="program_type_choice">
                 <param name="program_type" value="correct" />
                 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" ftype="fasta.gz"/>
@@ -83,14 +84,14 @@
             </conditional>
             <output name="corrected_read_file" file="lordec/corrected_reads.fa"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="program_type_choice">
                 <param name="program_type" value="trim" />
                 <param name="i" value="lordec/corrected_reads.fa" ftype="fasta"/>
             </conditional>
             <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="program_type_choice">
                 <param name="program_type" value="stats" />
                 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" />

diff --git a/tools/colibread/macros.xml b/tools/colibread/macros.xml
@@ -1,11 +1,10 @@
 <macros>
-    <token name="@DISCOSNP_VERSION@">2.5.4</token>
 
-    <token name="@PROFILE@">20.01</token>
+    <token name="@PROFILE@">23.1</token>
 
     <xml name="discosnp_requirements">
         <requirements>
-            <requirement type="package" version="@DISCOSNP_VERSION@">discosnp</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">discosnp</requirement>
         </requirements>
     </xml>
 

diff --git a/tools/colibread/mapsembler2.xml b/tools/colibread/mapsembler2.xml
@@ -1,10 +1,11 @@
-<tool id="mapsembler2" name="Mapsembler2" version="2.2.4+galaxy0" profile="@PROFILE@">
+<tool id="mapsembler2" name="Mapsembler2" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>is a targeted assembly software</description>
     <macros>
+        <token name="@TOOL_VERSION@">2.2.4</token>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="2.2.4">mapsembler2</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">mapsembler2</requirement>
     </requirements>
     <command><![CDATA[
         #import re
@@ -52,10 +53,10 @@
         <param argument="-y" type="integer" label="Max depth of nodes" value="10000" help="Set the maximal depth of the graph"/>
     </inputs>
     <outputs>
-        <data name="fasta" from_work_dir="res_k_*.fasta" format="fasta" label="Assembly with ${tool.name} on $on_string"/>
-        <data name="coherent" from_work_dir="res_coherent_*.fasta" format="fasta" label="Coherent with ${tool.name} on $on_string" hidden="true"/>
-        <data name="uncoherent" from_work_dir="res_uncoherent_*.fasta" format="fasta" label="Uncoherent with ${tool.name} on $on_string" hidden="true"/>
-        <data name="extremities" from_work_dir="starter_extremities.fa" format="fasta" label="Starter extremities with ${tool.name} on $on_string" hidden="true"/>
+        <data name="fasta" from_work_dir="res_k_*.fasta" format="fasta" label="${tool.name} on ${on_string}: Assembly"/>
+        <data name="coherent" from_work_dir="res_coherent_*.fasta" format="fasta" label="${tool.name} on ${on_string}: Coherent" hidden="true"/>
+        <data name="uncoherent" from_work_dir="res_uncoherent_*.fasta" format="fasta" label="${tool.name} on ${on_string}: Uncoherent" hidden="true"/>
+        <data name="extremities" from_work_dir="starter_extremities.fa" format="fasta" label="${tool.name} on ${on_string}: Starter extremities" hidden="true"/>
     </outputs>
     <tests>
         <test>