Mercurial > repos > devteam > fastx_quality_statistics
diff fastx_quality_statistics.xml @ 3:59003d0543cd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author | iuc |
---|---|
date | Tue, 08 May 2018 13:28:00 -0400 |
parents | 7306ec78632a |
children | cc0fd298cc17 |
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--- a/fastx_quality_statistics.xml Wed Nov 11 12:39:32 2015 -0500 +++ b/fastx_quality_statistics.xml Tue May 08 13:28:00 2018 -0400 @@ -1,19 +1,20 @@ -<tool id="cshl_fastx_quality_statistics" version="1.0.0" name="Compute quality statistics"> +<tool id="cshl_fastx_quality_statistics" version="1.0.1" name="Compute quality statistics"> <description></description> - <requirements> - <requirement type="package" version="0.0.13">fastx_toolkit</requirement> - </requirements> - <command> -<![CDATA[ -zcat -f < '$input' | fastx_quality_stats -o '$output' -Q 33 -]]> - </command> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +@CATS@ fastx_quality_stats +-o '$output' +@FQQUAL@ + ]]></command> <inputs> - <param format="fastqsanger" name="input" type="data" label="Library to analyse" /> + <expand macro="fastq_input" /> </inputs> <outputs> - <data format="txt" name="output" metadata_source="input" /> + <data name="output" format="txt" metadata_source="input" /> </outputs> <tests> <test> @@ -21,7 +22,7 @@ <output name="output" file="fastq_stats1.out" /> </test> </tests> - <help> + <help><![CDATA[ **What it does** Creates quality statistics report for the given Solexa/FASTQ library. @@ -52,7 +53,6 @@ * T_Count = Count of 'T' nucleotides found in this column. * N_Count = Count of 'N' nucleotides found in this column. - For example:: 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0 @@ -66,6 +66,7 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - </help> + ]]></help> + <expand macro="citations" /> <!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>