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changeset 2:1bb80c25b379 draft

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Uploaded
author stheil
date Thu, 24 Sep 2015 10:42:44 -0400
parents 0591d844bd08
children c979f8682b21
files velvet_macro.xml
diffstat 1 files changed, 147 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/velvet_macro.xml	Thu Sep 24 10:42:44 2015 -0400
@@ -0,0 +1,147 @@
+<macros>
+
+  <xml name="paired_library_options">
+    <param name="ins_length" type="integer" optional="true" label="Expected distance between two paired end reads"/>
+    <param name="ins_length_sd" type="integer" optional="true" label="Standard deviation for paired end reads length (default: 10% of corresponding length)"/>
+    <repeat min="1" name="files" title="Input files">
+      <conditional name="fileFormat">
+        <param name="format" type="select" label="File format">
+          <option value="-fasta">fasta</option>
+          <option value="-fastq">fastq</option>
+          <option value="-fasta_gz">fasta.gz</option>
+          <option value="-fastq_gz">fastq.gz</option>
+        </param>
+        <when value="-fasta">
+          <conditional name="fileLayout">
+            <param name="layout" type="select" label="File layout">
+              <option value="-interleaved">interleaved</option>
+              <option value="-separate">separate</option>
+            </param>
+            <when value="-interleaved">
+              <param name="sequence" type="data" format="fasta" label="Interleaved sequence file"/>
+            </when>
+            <when value="-separate">
+              <param name="sequence" type="data" format="fasta" label="Forward sequence file"/>
+              <param name="sequencePair" type="data" format="fasta" optional="true" label="Reverse sequence file"/>
+            </when>
+          </conditional>
+        </when>
+        <when value="-fasta_gz">
+          <conditional name="fileLayout">
+            <param name="layout" type="select" label="File layout">
+              <option value="-interleaved">interleaved</option>
+              <option value="-separate">separate</option>
+            </param>
+            <when value="-interleaved">
+              <param name="sequence" type="data" format="fasta.gz" label="Interleaved sequence file"/>
+            </when>
+            <when value="-separate">
+              <param name="sequence" type="data" format="fasta.gz" label="Forward sequence file"/>
+              <param name="sequencePair" type="data" format="fasta.gz" optional="true" label="Reverse sequence file"/>
+            </when>
+          </conditional>
+        </when>
+        <when value="-fastq">
+          <conditional name="fileLayout">
+            <param name="layout" type="select" label="File layout">
+              <option value="-interleaved">interleaved</option>
+              <option value="-separate">separate</option>
+            </param>
+            <when value="-interleaved">
+              <param name="sequence" type="data" format="fastq" label="Interleaved sequence file"/>
+            </when>
+            <when value="-separate">
+              <param name="sequence" type="data" format="fastq" label="Forward sequence file"/>
+              <param name="sequencePair" type="data" format="fastq" optional="true" label="Reverse sequence file"/>
+            </when>
+          </conditional>
+        </when>
+        <when value="-fastq_gz">
+          <conditional name="fileLayout">
+            <param name="layout" type="select" label="File layout">
+              <option value="-interleaved">interleaved</option>
+              <option value="-separate">separate</option>
+            </param>
+            <when value="-interleaved">
+              <param name="sequence" type="data" format="fastq.gz" label="Interleaved sequence file"/>
+            </when>
+            <when value="-separate">
+              <param name="sequence" type="data" format="fastq.gz" label="Forward sequence file"/>
+              <param name="sequencePair" type="data" format="fastq.gz" optional="true" label="Reverse sequence file"/>
+            </when>
+          </conditional>
+        </when>
+      </conditional>
+    </repeat>
+  </xml>
+
+  <token name="@PAIRED_FILES_OPTIONS@">
+
+    #for $j, $file in enumerate( $library.files )
+
+      $file.fileFormat.format
+
+      #if $file.fileFormat.fileLayout.layout == "-separate"
+        -separate $file.fileFormat.fileLayout.sequence $file.fileFormat.fileLayout.sequencePair
+      #else
+        -interleaved $file.fileFormat.fileLayout.sequence
+      #end if
+
+    #end for
+
+  </token>
+
+  <xml name="unpaired_library_options">
+    <repeat min="1" name="files" title="Input files">
+      <conditional name="fileFormat">
+        <param name="format" type="select" label="File format">
+          <option value="-fasta">fasta</option>
+          <option value="-fastq">fastq</option>
+          <option value="-raw">raw</option>
+          <option value="-fasta_gz">fasta.gz</option>
+          <option value="-fastq_gz">fastq.gz</option>
+          <option value="-raw_gz">raw.gz</option>
+          <option value="-sam">sam</option>
+          <option value="-bam">bam</option>
+        </param>
+        <when value="-fasta">
+          <param name="sequence" type="data" format="fasta" label="Sequence file"/>
+        </when>
+        <when value="-fasta_gz">
+          <param name="sequence" type="data" format="fasta.gz" label="Sequence file"/>
+        </when>
+        <when value="-fastq">
+          <param name="sequence" type="data" format="fastq" label="Sequence file"/>
+        </when>
+        <when value="-fastq_gz">
+          <param name="sequence" type="data" format="fastq.gz" label="Sequence file"/>
+        </when>
+        <when value="-raw">
+          <param name="sequence" type="data" format="txt" label="Sequence file"/>
+        </when>
+        <when value="-raw_gz">
+          <param name="sequence" type="data" format="txt" label="Sequence file"/>
+        </when>
+        <when value="-sam">
+          <param name="sequence" type="data" format="sam" label="Sequence file"/>
+        </when>
+        <when value="-bam">
+          <param name="sequence" type="data" format="bam" label="Sequence file"/>
+        </when>
+      </conditional>
+    </repeat>
+  </xml>
+
+  <token name="@UNPAIRED_FILES_OPTIONS@">
+
+    #for $j, $file in enumerate( $library.files )
+
+      $file.fileFormat.format
+
+      $file.fileFormat.sequence
+
+    #end for
+
+  </token>
+
+</macros>