Mercurial > repos > peterjc > fastq_paired_unpaired
diff tools/fastq/fastq_paired_unpaired.xml @ 2:95a632a71951 draft
Uploaded v0.0.6, adds unit test
author | peterjc |
---|---|
date | Tue, 30 Apr 2013 14:08:37 -0400 |
parents | 7ed81e36fc1c |
children | 528ba9c896e0 |
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--- a/tools/fastq/fastq_paired_unpaired.xml Mon Dec 12 11:33:10 2011 -0500 +++ b/tools/fastq/fastq_paired_unpaired.xml Tue Apr 30 14:08:37 2013 -0400 @@ -1,5 +1,6 @@ -<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.5"> +<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.6"> <description>using the read name suffices</description> + <version_command interpreter="python">fastq_paired_unpaired.py --version</version_command> <command interpreter="python"> fastq_paired_unpaired.py $input_fastq.extension $input_fastq #if $output_choice_cond.output_choice=="separate" @@ -9,6 +10,11 @@ #end if $output_singles </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> <inputs> <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/> <conditional name="output_choice_cond"> @@ -34,10 +40,20 @@ </data> </outputs> <tests> + <test> + <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/> + <param name="output_choice" value="separate"/> + <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/> + <output name="output_forward" file="sanger-pairs-forward.fastq" ftype="fastq"/> + <output name="output_reverse" file="sanger-pairs-reverse.fastq" ftype="fastq"/> + </test> + <test> + <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/> + <param name="output_choice" value="interleaved"/> + <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/> + <output name="output_paired" file="sanger-pairs-interleaved.fastq" ftype="fastq"/> + </test> </tests> - <requirements> - <requirement type="python-module">Bio</requirement> - </requirements> <help> **What it does**