Mercurial > repos > jjohnson > fastq_mcf
diff fastq-mcf.xml @ 1:b61f1466ce8f default tip
Add tool_dependencies.xml and test case
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Mon, 01 Apr 2013 10:28:17 -0500 |
parents | 217aedbdd0d0 |
children |
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--- a/fastq-mcf.xml Tue Mar 13 14:44:46 2012 -0400 +++ b/fastq-mcf.xml Mon Apr 01 10:28:17 2013 -0500 @@ -1,7 +1,7 @@ <tool id="fastq_mcf" name="FastqMcf" version="1.0"> <description>sequence quality filtering and clipping</description> <requirements> - <requirement type="binary">fastq-mcf</requirement> + <requirement type="package" version="1.1.2-484">ea-utils</requirement> </requirements> <version_string>fastq-mcf -V</version_string> <command>fastq-mcf @@ -41,7 +41,9 @@ #if len($trimming.sampcnt.__str__) > 0 -s $trimming.sampcnt #end if - $trimming.ilv3 + #if len($trimming.ilv3.__str__.strip()) > 0 + -$trimming.ilv3 + #end if $trimming.rmns #end if #if $noclip == True : @@ -120,9 +122,9 @@ </param> <param name="rmns" type="boolean" truevalue="-R" falsevalue="" checked="false" label="-R Don't remove N's from the fronts/ends of reads"/> <param name="ilv3" type="select" label="illumina PF filtering"> - <option value=" ">Default</option> - <option value="-U">Disable illumina PF filtering</option> - <option value="-u">Enable illumina PF filtering</option> + <option value="">Default</option> + <option value="U">Disable illumina PF filtering</option> + <option value="u">Enable illumina PF filtering</option> </param> </when> </conditional> @@ -143,7 +145,24 @@ <filter>(noclip == False and mates != None)</filter> </data> </outputs> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> <tests> + <test> + <param name="adpaters" ftype="fasta" value="adapters.fa" /> + <param name="reads" ftype="fastqillumina" value="test_mcf_reads.fq" /> + <param name="mates" ftype="fastqillumina" value="test_mcf_mates.fq" /> + <param name="choice" value="user_set" /> + <param name="nkeep" value="16" /> + <param name="qthr" value="15" /> + <param name="qwin" value="5" /> + <param name="pctns" value="10" /> + <param name="ilv3" value="u" /> + <param name="phred" value="33" /> + <output name="reads_out" file="testout_mcf_reads.fq" /> + <output name="mates_out" file="testout_mcf_mates.fq" /> + </test> </tests> <help> **What it does** @@ -156,6 +175,8 @@ Detect N's, and remove from ends Remove reads with CASAVA 'Y' flag (purity filtering) Discard sequences that are too short after all of the above + + Keep multiple mate-reads in sync while doing all of the above .. _fastq-mcf: http://code.google.com/p/ea-utils/wiki/FastqMcf