Mercurial > repos > iuc > khmer_filter_below_abundance_cutoff
view filter-below-abund.xml @ 1:e0e33e40d7c4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
author | iuc |
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date | Wed, 11 Nov 2015 10:05:04 -0500 |
parents | 67b597ec0baf |
children | bf716cfc3225 |
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<tool id="khmer_filter_below_abundance_cutoff" name="Filter reads" version="@WRAPPER_VERSION@.0"> <description> below k-mer abundance of 50 </description> <macros> <token name="@BINARY@">filter-below-abund.py</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ #for $num, $input in enumerate($inputs) ln -s ${input} sequence-${num} && #end for mkdir output && cd output && $__tool_directory__/@BINARY@ ${input_countgraph_filename} #for $num, $input in enumerate($inputs) ../sequence-${num} #end for ]]> </command> <inputs> <expand macro="input_sequences_filenames" /> <expand macro="input_countgraph_filename" /> </inputs> <outputs> <collection name="sequence_files" type="list"> <discover_datasets pattern="__name__" directory="output" /> </collection> </outputs> <tests> <test> <param name="inputs" value="test-abund-read-2.fa" /> <param name="input_countgraph_filename" value="test-abund-read-2.large.oxlicg" ftype="oxlicg" /> <output_collection name="sequence_files"> <element name="sequence-0.below" file="test-abund-read-2.fa.below" /> </output_collection> </test> </tests> <help><![CDATA[ Trims fastq/fasta sequences at k-mers with abundance below 50 based on a provided k-mer countgraph. @HELP_FOOTER@ ]]></help> <citations> <expand macro="software-citation" /> <expand macro="counting-citation" /> </citations> </tool>