Mercurial > repos > iuc > ivar_filtervariants
view ivar_filtervariants.xml @ 3:2c47c138176e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 47276c84cd0cd40084b7ccdf2e22c620ee1c10f6"
author | iuc |
---|---|
date | Fri, 05 Jun 2020 04:15:12 -0400 |
parents | c88553ec696e |
children | 72ddd32392cd |
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<tool id="ivar_filtervariants" name="ivar filtervariants" version="@VERSION@+galaxy0"> <description>Filter variants across replicates or multiple samples aligned using the same reference</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ #for $counter, $input in enumerate($inputs): ln -s '$input' ./var_${counter}.tsv && #end for ivar filtervariants -p filtered.tsv #for $counter, $input in enumerate($inputs) ./var_${counter}.tsv #end for ]]></command> <inputs> <param name="inputs" type="data" format="tabular" multiple="true" label="Variant tsv files for each replicate"/> </inputs> <outputs> <data name="output_filtered" format="tabular" label="${tool.name} on ${on_string}" from_work_dir="filtered.tsv"/> </outputs> <tests> <test> <param name="inputs" value="zika/Z52_a.tsv,zika/Z52_b.tsv" ftype="tabular"/> <output name="output_filtered" file="zika/Z52.tsv" ftype="tabular" lines_diff="10"/> </test> </tests> <help><![CDATA[ iVar can be used to get an intersection of variants(in .tsv files) called from any number of replicates or from different samples using the same reference sequence. This intersection will filter out any iSNVs that do not occur in a minimum fraction of the files supplied. This parameter can be changed using the -t flag which range from 0 to 1 (default). Fields that are different across replicates(fields apart from REGION, POS, REF, ALT, REF_CODON, REF_AA, ALT_CODON, ALT_AA) will have the filename added as a suffix. If there are a large number of files to be filtered, the -f flag can be used to supply a text file with one sample/replicate variant .tsv file per line. Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_. ]]></help> <expand macro="citations" /> </tool>