diff velvet.xml @ 0:d81360ea69d8 draft

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/velvet.xml	Tue Jun 28 17:30:32 2016 -0400
@@ -0,0 +1,120 @@
+<tool id="velvet" name="velvet" version="0.1.0">
+    <requirements>
+      <requirement type="package" version="1.2.10">velvet</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+    <command><![CDATA[
+        velveth
+          out
+          $kmer
+          #for $i in $files:
+            -${i.filetype}
+
+            #if str($i.paired_type.paired_type_selector) == "paired":
+
+              #if $i.__index__ > 1:
+                -shortPaired$i.__index__
+              #else
+              -shortPaired
+              #end if
+
+              -separate $i.paired_type.input1 $i.paired_type.input2
+            #end if
+
+            #if str($i.paired_type.paired_type_selector) == "single"
+
+              #if $i.__index__ > 1
+                -short$i.__index__
+              #else
+                -short
+              #end if
+
+              $i.paired_type.input1
+            #end if
+
+            #if str($i.paired_type.paired_type_selector) == "paired_collection"
+              #if $i.__index__ > 1
+                -shortPaired$i.__index__
+              #else
+                -shortPaired
+              #end if
+              -separate $i.paired_type.input1.forward $i.paired_type.input1.reverse
+            #end if
+            #if str($i.paired_type.paired_type_selector) == "paired_iv"
+              #if $i.__index__ > 1
+                -shortPaired$i.__index__
+              #else
+                -shortPaired
+              #end if
+              $i.paired_type.input1
+            #end if
+          #end for
+          
+          && 
+          
+          velvetg out > $log
+    ]]></command>
+    <inputs>
+      <param name="kmer" type="integer" value="29" label="K-mer" help="The kmer value to use for velvet - must be an odd integer between 19 and 191" />
+      <repeat name="files" title="Input files" min="1">
+        <param name="filetype" label="Input file type" type="select" help="Input file type">
+          <option value="fastq">Fastq</option>
+          <option value="fasta">Fasta</option>
+          <option value="bam">Bam</option>
+        </param>
+        <conditional name="paired_type">
+          <param name="paired_type_selector" type="select" label="Single or paired end reads" help="Select between paired and single end data">
+            <option value="paired">Paired</option>
+            <option value="single">Single</option>
+            <option value="paired_collection">Paired Collection</option>
+            <option value="paired_iv">Paired Interleaved</option>
+          </param>
+          <when value="paired">
+            <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select first set of reads" help="Specify dataset with forward reads"/>
+            <param name="input2" type="data" format="fastqsanger,fasta,bam" label="Select second set of reads" help="Specify dataset with reverse reads"/>
+          </when>
+          <when value="single">
+            <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select the reads" help="Specify dataset with the reads"/>
+          </when>
+          <when value="paired_collection">
+            <param name="input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
+          </when>
+          <when value="paired_iv">
+            <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select set of interleaved reads" help="Specify dataset with interleaved paired reads"/>
+          </when>
+        </conditional>
+      </repeat>
+      
+    </inputs>
+    <outputs>
+      <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/>
+      <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Contig Stats" from_work_dir="out/stats.txt"/>
+      <data format="tabular" name="graph" label="${tool.name} on ${on_string}: Last Graph" from_work_dir="out/LastGraph"/>
+      <data format="tabular" name="log" label="${tool.name} on ${on_string}: log" />
+    </outputs>
+    <tests>
+      <test>
+        <param name="kmer" value="29" />
+        <param name="files_0|filetype" value="fasta" />
+        <param name="files_0|paired_type|paired_type_selector" value="single" />
+        <param name="files_0|paired_type|input1" value="test_reads.fa" ftype="fasta" />
+        <output name="contigs" ftype="fasta" file="contigs.fa" />
+      </test>
+    </tests>
+    <help><![CDATA[
+        The Velvet wrapper, wraps both velveth and velvetg for single kmer value with no parameters supplied to velvetg. It is mainly for teaching how kmer size affects the assembly. 
+        
+        It returns the contigs.fa file, the contig_stats.txt file, the LastGraph file and captures the screen output to the log.
+        
+        This tool is mainly wrapped for assembly teaching purposes. It should not be used for actual assemblies. Please use the Velvet Optimiser for this purpose.
+        
+        The kmer value supplied needs to be an odd integer.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1101/gr.074492.107</citation>
+        <citation type="doi">10.1371/journal.pone.0008407</citation>
+    </citations>
+</tool>
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