diff sopra_wpc.xml @ 2:87ffe493b6c1 draft default tip

Use GALAXY_SLOTS for multithreading in Bowtie. Create symlinks instead of copying files. Specify in help that Bowtie is used to align the reads to the contigs. Add readme.rst .

--- a/sopra_wpc.xml	Tue Oct 29 05:27:29 2013 -0400
+++ b/sopra_wpc.xml	Mon Mar 03 11:28:41 2014 -0500
@@ -1,11 +1,11 @@
 <tool id="sopra_wpc" name="SOPRA with prebuilt contigs" version="0.1">
-  <description>for Illumina workflow</description>
+  <description>for Illumina libraries</description>
   <requirements>
     <requirement type="package" version="1.4.6">sopra</requirement>
     <requirement type="package" version="1.0.0">bowtie</requirement>
   </requirements>
   <command interpreter="python">
-    sopra_wpc.py
+    sopra_wpc.py -p \${GALAXY_SLOTS:-1}
     #for $cr in $contigs_repeat
       --contigs ${cr.contigs_file}
     #end for
@@ -36,7 +36,9 @@
   <help>
 **What it does**
 
-SOPRA is an assembly tool for mate pair/paired-end data generated by high-throughput sequencing technologies, e.g. Illumina and SOLiD platforms.
+SOPRA is a scaffold assembly tool for paired-end/mate pair data generated by high-throughput sequencing technologies, e.g. Illumina and SOLiD platforms. This wrapper currently supports only Illumina paired-end data.
+
+Bowtie is used to align the reads to the contigs.
 
 The input paired-end FASTA file can be obtained with:
 FR reads -> *FASTQ interlacer on paired end reads* followed by *FASTQ to FASTA* converter