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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
author iuc
date Wed, 25 Sep 2024 14:12:43 +0000
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1 <tool id="chewbbaca_joinprofiles" name="chewBBACA JoinProfiles" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Join allele calling results from different runs</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 chewBBACA.py JoinProfiles
9 -p ${str($input1).replace(',', ' ')}
10 -o 'JoinedProfile.tsv'
11 $common
12 ]]></command>
13 <inputs>
14 <param name="input1" type="data" format="tsv" multiple="true" label="AlleleCall results" />
15 <param argument="--common" type="boolean" truevalue="--common" falsevalue="" checked="false" label="Common" optional="true" help="Create file with profiles for the set of common loci" />
16 </inputs>
17 <outputs>
18 <data format="tabular" name="JoinedProfile" from_work_dir="JoinedProfile.tsv" label="${tool.name} on ${on_string}: Joined profiles"/>
19 </outputs>
20 <tests>
21 <test>
22 <param name="input1" value="results_alleles.tsv,results_alleles2.tsv"/>
23 <output name="JoinedProfile" file="JoinedProfile.tsv" compare="diff"/>
24 </test>
25 </tests>
26 <help>
27 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
28
29 The process creates a TSV file with the allelic profiles of all samples in the input files.
30
31 .. class:: infomark
32
33 **Important**
34
35 It is necessary to pass the --common argument if the input files do not have the same set of loci (this option creates a new file only with the set of loci shared between all input files).
36 </help>
37 <expand macro="citations" />
38 </tool>