Mercurial > repos > devteam > fastq_quality_filter
diff fastq_quality_filter.xml @ 3:43a7370aa010 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
| author | iuc |
|---|---|
| date | Tue, 08 May 2018 13:26:35 -0400 |
| parents | e41385662e5e |
| children | 7b4468117008 |
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--- a/fastq_quality_filter.xml Wed Nov 11 12:37:55 2015 -0500 +++ b/fastq_quality_filter.xml Tue May 08 13:26:35 2018 -0400 @@ -1,30 +1,28 @@ -<tool id="cshl_fastq_quality_filter" version="1.0.0" name="Filter by quality"> +<tool id="cshl_fastq_quality_filter" version="1.0.1" name="Filter by quality"> <description></description> - <requirements> - <requirement type="package" version="0.0.13">fastx_toolkit</requirement> - </requirements> - <command> -<![CDATA[ -zcat -f < '$input' | fastq_quality_filter -q $quality -p $percent -v -o '$output' -#if $input.ext == "fastqsanger": - -Q 33 -#end if -]]> - </command> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +@CATS@ fastq_quality_filter +-q $quality +-p $percent +-v +-o '$output' +@FQQUAL@ + ]]></command> <inputs> - <param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to filter" /> + <expand macro="fastq_input" /> - <param name="quality" type="integer" value="20"> - <label>Quality cut-off value</label> - </param> + <param name="quality" type="integer" value="20" label="Quality cut-off value"/> - <param name="percent" type="integer" value="90"> - <label>Percent of bases in sequence that must have quality equal to / higher than cut-off value</label> - </param> + <param name="percent" type="integer" value="90" + label="Percent of bases in sequence that must have quality equal to / higher than cut-off value" /> </inputs> <outputs> - <data format_source="input" name="output" metadata_source="input" /> + <data name="output" format_source="input" metadata_source="input" /> </outputs> <tests> <test> @@ -42,7 +40,7 @@ <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1b.out" /> </test> </tests> - <help> + <help><![CDATA[ **What it does** This tool filters reads based on quality scores. @@ -78,6 +76,7 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - </help> + ]]></help> + <expand macro="citations" /> <!-- FASTQ-Quality-Filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>