Mercurial > repos > iuc > ivar_filtervariants
diff ivar_filtervariants.xml @ 0:c88553ec696e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
author | iuc |
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date | Mon, 30 Mar 2020 07:18:00 -0400 |
parents | |
children | 72ddd32392cd |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ivar_filtervariants.xml Mon Mar 30 07:18:00 2020 -0400 @@ -0,0 +1,45 @@ +<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>