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changeset 4:e0e4fc474b07 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet commit 46fdfdaee17ad325380feb4bb54d4fd143a9ba4f
author iuc
date Mon, 04 Aug 2025 14:38:15 +0000
parents 920677cd220f
children
files macros.xml velvetg.xml velveth.xml
diffstat 3 files changed, 62 insertions(+), 40 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Sun Jan 24 15:40:17 2021 +0000
+++ b/macros.xml	Mon Aug 04 14:38:15 2025 +0000
@@ -6,15 +6,16 @@
       </requirements>
   </xml>
   <token name="@WRAPPER_VERSION@">1.2.10</token>
+  <token name="@PROFILE@">24.0</token>
   <xml name="stdio">
     <stdio>
       <!-- Anything other than zero is an error -->
       <exit_code level="fatal" range="1:"/>
       <exit_code level="fatal" range=":-1"/>
-      <!-- In case the return code has not been set propery check stderr too -->
+      <!-- In case the return code has not been set properly check stderr too -->
       <regex level="fatal" match="Error:" source="both" />
       <regex level="fatal" match="Exception:" source="both" />
-      <regex level="fatal_oom" match="Can't calloc" source="both" />
+      <regex level="fatal_oom" match="Can't alloc" source="both" />
     </stdio>
   </xml>
   <xml name="citation">
@@ -24,5 +25,17 @@
           </citation>
       </citations>
   </xml>
+  <token name="@WHATITDOES@">
+**What it does**
+
+Velvet is a de novo genomic assembler specially designed for short-read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the
+European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
+
+Velvet currently takes in short read sequences, removes errors, and then produces high-quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
+
+Read the Velvet `documentation`__ for details on using the Velvet Assembler.
+
+.. __: https://github.com/dzerbino/velvet/blob/master/Manual.pdf
+  </token>
 </macros>
 
--- a/velvetg.xml	Sun Jan 24 15:40:17 2021 +0000
+++ b/velvetg.xml	Mon Aug 04 14:38:15 2025 +0000
@@ -1,8 +1,11 @@
-<tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.2">
+<tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.3" profile="@PROFILE@">
   <description>Velvet sequence assembler for very short reads</description>
   <macros>
     <import>macros.xml</import>
   </macros>
+  <xrefs>
+      <xref type="bio.tools">velvet</xref>
+  </xrefs>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
   <version_command><![CDATA[
@@ -198,11 +201,19 @@
         <composite_data value='velvetg_paired/Log'/>
       </param>
       <param name="add_out" value="amos,unused,lastgraph" />
-      <param name="read_trkg" value="-read_trkg no" />
-      <param name="cutoff" value="auto" />
-      <param name="coverage" value="auto" />
-      <param name="use_contig_lgth" value="no" />
-      <param name="paired" value="no" />
+      <param name="read_trkg" value="false" />
+      <conditional name="coverage">
+        <param name="cutoff" value="auto" />
+      </conditional>
+      <conditional name="expected">
+        <param name="coverage" value="auto" />
+      </conditional>
+      <conditional name="contig_lgth">
+        <param name="use_contig_lgth" value="no" />
+      </conditional>
+      <conditional name="reads">
+        <param name="paired" value="no" />
+      </conditional>
       <output name="velvet_asm" file="velvetg_paired/velvet_asm.afg" compare="diff"/>
       <output name="unused_reads_fasta" file="velvetg_paired/UnusedReads.fa" compare="diff"/>
       <output name="LastGraph" file="velvetg_paired/lastgraph.txt" compare="diff"/>
@@ -211,17 +222,7 @@
     </test>
   </tests>
   <help><![CDATA[
-**What it does**
-
-Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
-
-Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
-
-Read the Velvet `documentation`__ for details on using the Velvet Assembler.
-
-.. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
-
-.. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
+@WHATITDOES@
 
 ------
 
--- a/velveth.xml	Sun Jan 24 15:40:17 2021 +0000
+++ b/velveth.xml	Mon Aug 04 14:38:15 2025 +0000
@@ -1,8 +1,11 @@
-<tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.3">
+<tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.4" profile="@PROFILE@">
   <description>Prepare a dataset for the Velvet velvetg Assembler</description>
   <macros>
     <import>macros.xml</import>
   </macros>
+  <xrefs>
+      <xref type="bio.tools">velvet</xref>
+  </xrefs>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
   <version_command><![CDATA[
@@ -81,14 +84,22 @@
         <conditional name="input_type">
           <param name="input_type_selector" value="paireds" />
           <param name="read_type" value="-shortPaired" />
-          <param name="input1" value="R1.fastq" ftype="fastqsanger" />
+          <param name="input" value="R1.fastq" ftype="fastqsanger" />
           <param name="input2" value="R2.fastq" ftype="fastqsanger" />
         </conditional>
       </repeat>
-      <param name="strand_specific" value="" />
+      <param name="strand_specific" value="false" />
       <output name="outfile" file="velveth_paireds.out">
-        <extra_files type="file" name='Sequences' value="velveth_paireds/Sequences" compare="diff" />
-        <extra_files type="file" name='Roadmaps' value="velveth_paireds/Roadmaps" compare="diff" />
+        <extra_files type="file" name='Sequences' value="velveth_paireds/Sequences" compare="sim_size">
+          <assert_contents>
+            <has_line_matching expression="^>mutant-no_snps.gff.*"/>
+          </assert_contents>
+        </extra_files>
+        <extra_files type="file" name='Roadmaps' value="velveth_paireds/Roadmaps" compare="sim_size">
+          <assert_contents>
+            <has_text text="ROADMAP"/>
+          </assert_contents>
+        </extra_files>
       </output>
     </test>
     <test>
@@ -100,10 +111,14 @@
           <param name="input" value="R1.fastq" ftype="fastqillumina" />
         </conditional>
       </repeat>
-      <param name="strand_specific" value="" />
+      <param name="strand_specific" value="false" />
       <output name="outfile" file="velveth_single.out">
         <extra_files type="file" name='Sequences' value="velveth_single/Sequences" compare="diff" />
-        <extra_files type="file" name='Roadmaps' value="velveth_single/Roadmaps" compare="diff" />
+        <extra_files type="file" name='Roadmaps' value="velveth_single/Roadmaps" compare="sim_size">
+          <assert_contents>
+            <has_text text="ROADMAP"/>
+          </assert_contents>
+        </extra_files>
       </output>
     </test>
     <test>
@@ -116,32 +131,25 @@
         </conditional>
       </repeat>
       <repeat name="inputs">
-        <param name="file_format" value="fastq" />
         <conditional name="input_type">
           <param name="input_type_selector" value="single" />
           <param name="read_type" value="-short2" />
           <param name="input" value="R2.fastq" ftype="fastq" />
         </conditional>
       </repeat>
-      <param name="strand_specific" value="" />
+      <param name="strand_specific" value="false" />
       <output name="outfile" file="velveth_single.out">
         <extra_files type="file" name='Sequences' value="velveth_single2/Sequences" compare="diff" />
-        <extra_files type="file" name='Roadmaps' value="velveth_single2/Roadmaps" compare="diff" />
+        <extra_files type="file" name='Roadmaps' value="velveth_single2/Roadmaps" compare="sim_size">
+          <assert_contents>
+            <has_text text="ROADMAP"/>
+          </assert_contents>
+        </extra_files>
       </output>
     </test>
   </tests>
   <help><![CDATA[
-**What it does**
-
-Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
-
-Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
-
-Read the Velvet `documentation`__ for details on using the Velvet Assembler.
-
-.. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
-
-.. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
+@WHATITDOES@
 
 ------