Mercurial > repos > devteam > fastx_artifacts_filter
diff fastx_artifacts_filter.xml @ 3:dd3737e40dce draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author | iuc |
---|---|
date | Tue, 08 May 2018 13:27:02 -0400 |
parents | 09070cacefd8 |
children | 567d5b3c52b1 |
line wrap: on
line diff
--- a/fastx_artifacts_filter.xml Wed Nov 11 12:38:23 2015 -0500 +++ b/fastx_artifacts_filter.xml Tue May 08 13:27:02 2018 -0400 @@ -1,22 +1,21 @@ -<tool id="cshl_fastx_artifacts_filter" version="1.0.0" name="Remove sequencing artifacts"> +<tool id="cshl_fastx_artifacts_filter" version="1.0.1" name="Remove sequencing artifacts"> <description></description> - <requirements> - <requirement type="package" version="0.0.13">fastx_toolkit</requirement> - </requirements> - <command> -<![CDATA[ -zcat -f < '$input' | fastx_artifacts_filter -v -o '$output' -#if $input.ext == "fastqsanger": - -Q 33 -#end if -]]> - </command> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +@CATS@ fastx_artifacts_filter +-v +-o '$output' +@FQQUAL@ + ]]></command> <inputs> - <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" /> + <expand macro="fastx_input" /> </inputs> <outputs> - <data format_source="input" name="output" metadata_source="input" /> + <data name="output" format_source="input" metadata_source="input" /> </outputs> <tests> <test> @@ -30,7 +29,7 @@ <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" /> </test> </tests> - <help> + <help><![CDATA[ **What it does** This tool filters sequencing artifacts (reads with all but 3 identical bases). @@ -87,6 +86,7 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - </help> + ]]></help> + <expand macro="citations" /> <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>