Mercurial > repos > iuc > tn93_filter
view tn93_filter.xml @ 0:ba95715078c9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
author | iuc |
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date | Fri, 23 Apr 2021 03:05:08 +0000 |
parents | |
children | cf50aeb956f2 |
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<tool id="tn93_filter" name="TN93 Filter" version="@VERSION@"> <description>- remove sequences from a reference that are within a given distance of of a cluster</description> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="@VERSION@">tn93</requirement> <requirement type="package" version="1.70">biopython</requirement> </requirements> <version_command><![CDATA[tn93 --version]]></version_command> <command detect_errors="exit_code"><![CDATA[ cat '$reads' > filtered_msa.fa && tn93 -o pairwise.csv -s filtered_msa.fa -t $threshold '$clusters' && python '$__tool_directory__/tn93_filter.py' --reference '$reference' --distances pairwise.csv --reads filtered_msa.fa --clusters '$clusters' ]]></command> <inputs> <param name="reads" type="data" format="fasta" label="Aligned reads" /> <param name="reference" type="data" format="fasta" label="Reference sequence" /> <param name="clusters" type="data" format="fasta" label="FASTA file with compressed clusters" /> <param name="threshold" type="float" value="0.015" label="Pairwise distance threshold" /> </inputs> <outputs> <data name="filtered_reference" format="fasta" from_work_dir="filtered_msa.fa" /> </outputs> <tests> <test> <param name="reads" value="filter-in1-reads.fa" /> <param name="reference" value="filter-in1-reference.fa" /> <param name="clusters" value="filter-in1-clusters.fa" /> <param name="threshold" value="0.35" /> <output name="filtered_reference" file="filter-out1.fasta" ftype="fasta" /> </test> </tests> <help><![CDATA[ TN93-Filter =========== Removes aligned sequences that are within a given distance from a reference sequence using the 1993 Tamura-Nei distance calculation. ]]></help> <expand macro="citations"> <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation> </expand> </tool>