Mercurial > repos > iuc > khmer_filter_abundance
view filter-abund.xml @ 3:88740fc6d206 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit bfa8bda732de882f6fa5f5375f8468ad229cceea
author | iuc |
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date | Wed, 09 Nov 2016 05:58:22 -0500 |
parents | 03246d4ea8cd |
children | 8c6433857aa8 |
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<tool id="khmer_filter_abundance" name="Filter reads" version="@WRAPPER_VERSION@.0"> <description> by minimal k-mer abundance </description> <macros> <token name="@BINARY@">filter-abund.py</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version" /> <command><![CDATA[ set -xu && #for $num, $input in enumerate($inputs) ln -s ${input} filter-abund-sequence-${num} && #end for mkdir output && cd output && @BINARY@ --cutoff=${cutoff} ${variable_coverage} @THREADS@ ${input_countgraph_filename} ../filter-abund-sequence* ]]> </command> <inputs> <expand macro="input_sequences_filenames" /> <param name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue="" label="Variable coverage" help="Only trim when a sequence has high enough coverage; median abundance > 20 (--variable_coverage)" /> <param name="cutoff" type="integer" value="2" label="Cutoff" help="Trim at k-mers below this abundance. (--cutoff)" /> <expand macro="input_countgraph_filename" /> </inputs> <outputs> <collection name="filter-abund-sequences" 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.oxlicg" ftype="oxlicg" /> <output_collection name="filter-abund-sequences" type="list"> <element name="filter-abund-sequence-0.abundfilt"> <assert_contents> <has_text text="GGTTGACGGGGCTCAGGG" /> </assert_contents> </element> </output_collection> </test> <test> <param name="inputs" value="test-abund-read-2.fa" /> <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" /> <param name="cutoff" value="1" /> <output_collection name="filter-abund-sequences" type="list"> <element name="filter-abund-sequence-0.abundfilt"> <assert_contents> <has_text text="GGTTGACGGGGCTCAGGG" /> </assert_contents> </element> </output_collection> </test> </tests> <help><![CDATA[ Trims fastq/fasta sequences at k-mers of a given abundance based on a provided k-mer countgraph If the input sequences are from RNAseq or metagenome sequencing then `--variable-coverage` should be used. @HELP_FOOTER@ ]]> </help> <citations> <expand macro="software-citation" /> <expand macro="counting-citation" /> </citations> </tool>