Mercurial > repos > nilesh > sickle
diff sickle.xml @ 6:c6a790326d1e
moved from test
author | nilesh |
---|---|
date | Mon, 15 Jul 2013 12:12:41 -0500 |
parents | 98e35d7ce5c9 |
children | dd2ec1b37e96 |
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--- a/sickle.xml Fri Jul 12 14:01:18 2013 -0500 +++ b/sickle.xml Mon Jul 15 12:12:41 2013 -0500 @@ -1,7 +1,6 @@ <tool id="sickle" name="Sickle"> <description>Windowed Adaptive Trimming of FastQ data</description> <requirements> - <requirement type="package" version="1.2.8">zlib</requirement> <requirement type="package" version="1.21.0">sickle</requirement> </requirements> <command> @@ -84,7 +83,20 @@ <filter>(readtype['single_or_paired'] == 'pe')</filter> </data> </outputs> - + <tests> + <param name="single_or_paired" value="pe"/> + <param name="input_paired1" value="test.f.fastq"/> + <param name="input_paired2" value="test.r.fastq"/> + <param name="qual_type" value="illumina"/> + <param name="qual_threshold" value="20"/> + <param name="length_threshold" value="20"/> + <param name="no_five_prime" value="false"/> + <param name="discard_n" value="false"/> + <output name="output_paired1" value="output.f.fastq"/> + <output name="output_paired2" value="output.r.fastq"/> + <output name="output_paired_single" value="output.fastq"/> + </tests> + <help> Most modern sequencing technologies produce reads that have deteriorating quality towards the 3'-end and some towards the 5'-end as well. Incorrectly called bases in both regions negatively impact assembles, mapping, and downstream bioinformatics analyses.