Mercurial > repos > iuc > khmer_filter_below_abundance_cutoff
view filter-below-abund.xml @ 10:00f7064c564b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
author | iuc |
---|---|
date | Thu, 03 Oct 2024 13:46:21 +0000 |
parents | 19607c740d19 |
children |
line wrap: on
line source
<tool id="khmer_filter_below_abundance_cutoff" name="khmer: Filter reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description> below k-mer abundance of 50 </description> <macros> <token name="@BINARY@">filter-below-abund.py</token> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> <expand macro="requirements"> <requirement type="package" version="1.0.1">screed</requirement> </expand> <expand macro="stdio" /> <command><![CDATA[ @LINK_SEQUENCES@ mkdir output && cd output && python '$__tool_directory__/@BINARY@' '${input_countgraph_filename}' @USE_SEQUENCES@ ]]> </command> <inputs> <expand macro="input_sequences_filenames" /> <expand macro="input_countgraph_filename" /> </inputs> <outputs> <expand macro="output_sequences" extension="below"/> </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="sequences"> <element name="test-abund-read-2.fa" 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>