diff tools/rtg/format_fastq.xml @ 1:8593828f91e7 default tip

Full galaxy wrapper

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rtg/format_fastq.xml	Sat Apr 21 21:36:15 2012 -0400
@@ -0,0 +1,48 @@
+<tool id="rtg_format_fastq" name="Format FASTQ">
+  <description>to SDF with rtg format</description>
+  <command interpreter="bash">galaxy-rtg-wrapper.sh format
+-f fastq 
+#if $paired.sPaired == "paired":
+-l $paired.input1
+-r $paired.input2 
+#else:
+$paired.input1
+#end if
+#if str($protein) == "true":
+-p
+#end if
+-q $quality_format
+-o ${output.extra_files_path} >$output</command>
+  <inputs>
+    <conditional name="paired">
+      <param name="sPaired" type="select" label="Are you formatting paired-end reads?">
+        <option value="single">Non-read data or single-end</option>
+        <option value="paired">Paired-end</option>
+      </param>
+      <when value="single">
+        <param name="input1" type="data" format="fastq" label="Source FASTQ file"/>
+      </when>
+      <when value="paired">
+        <param name="input1" type="data" format="fastq" label="First of pair FASTA file"/>
+        <param name="input2" type="data" format="fastq" label="Second of pair FASTA file"/>
+      </when>
+    </conditional>
+    <param name="quality_format" type="select" label="Quality format">
+      <option value="sanger" selected="true">Sanger</option>
+      <option value="solexa">Solexa</option>
+      <option value="illumina">Illumina</option>
+    </param>	
+    <param name="protein" type="select" label="Input consists of protein">
+      <option value="false" selected="true">False</option>
+      <option value="true">True</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="rtg_sdf" name="output" />
+  </outputs>
+
+  <help>
+This tool formats a FASTQ file to RTG SDF.
+  </help>
+
+</tool>