Mercurial > repos > iuc > chewbbaca_extractcgmlst

comparison ExtractCgMLST.xml @ 1:a302f0fef852 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 2564b0ca982636c6c6f221d0c5072f52d39e6751
author iuc
date Sat, 11 May 2024 22:50:28 +0000
parents 743125c3ac12
children
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0:743125c3ac12 1:a302f0fef852
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 mkdir 'input' &&
9 #for $file in $input_file
10 ln -sf '$file' 'input/${file.element_identifier}.tsv' &&
11 #end for
12 chewBBACA.py ExtractCgMLST 8 chewBBACA.py ExtractCgMLST
13 --t $threshold 9 --t $threshold
14 #if str($genes2remove) != 'false' 10 #if $genes2remove:
15 --r 'input/paralogous_counts.tsv' 11 --r '$genes2remove'
16 #end if 12 #end if
17 #if $genomes2remove: 13 #if $genomes2remove:
18 --g '$genomes2remove' 14 --g '$genomes2remove'
19 #end if 15 #end if
20 -i 'input/results_alleles.tsv' -o 'output' 16 -i '$input_file' -o 'output'
21 ]]></command> 17 ]]></command>
22 <inputs> 18 <inputs>
23 <param name="input_file" type="data_collection" collection_type="list" label="AlleleCall Results" format="tabular"/> 19 <param argument="--input-file" type="data" label="Allelic Profiles" format="tabular"/>
24 <section name="advanced" title="Advanced options"> 20 <section name="advanced" title="Advanced options">
25 <param argument="--genomes2remove" type="data" format="txt" label="Genomes/rows to remove from the matrix" optional="true" help="One genome identifier per line"/> 21 <param argument="--genomes2remove" type="data" format="txt" label="Genomes/rows to remove from the matrix" optional="true" help="One genome identifier per line"/>
26 <param argument="--threshold" type="text" value="0.95 0.99 1" label="threshold" help="Genes that constitute the core genome must be in a proportion of genomes that is at least equal to this value. Users can provide multiple values as a space-separated list."> 22 <param argument="--threshold" type="text" value="0.95 0.99 1" label="threshold" help="Genes that constitute the core genome must be in a proportion of genomes that is at least equal to this value. Users can provide multiple values as a space-separated list.">
27 <validator type="regex">[ .0-9]+</validator> 23 <validator type="regex">[ .0-9]+</validator>
28 </param> 24 </param>
29 <param name="genes2remove" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove paralogous counts?" help="the list of genes listed in the &quot;paralogous_counts.tsv&quot; file created by the AlleleCall process. --genes2remove"/> 25 <param argument="--genes2remove" type="data" format="tabular" label="List of genes to exclude from analysis" optional="true" help="the list of genes listed in the &quot;paralogous_counts.tsv&quot; file created by the AlleleCall process."/>
30 </section> 26 </section>
31 </inputs> 27 </inputs>
32 <outputs> 28 <outputs>
33 <collection name="output_collection" type="list" format="html,tsv,txt" label="${tool.name} on ${on_string}"> 29 <collection name="output_collection" type="list" format="html,tsv,txt" label="${tool.name} on ${on_string}">
34 <discover_datasets pattern="__name_and_ext__" directory="output"/> 30 <discover_datasets pattern="__name_and_ext__" directory="output"/>
35 </collection> 31 </collection>
36 </outputs> 32 </outputs>
37 <tests> 33 <tests>
38 <test> 34 <test>
39 <param name="input_file"> 35 <param name="input_file" value="results_alleles.tsv"/>
40 <collection type="list">
41 <element name="results_alleles" value="results_alleles.tsv" ftype="tabular"/>
42 </collection>
43 </param>
44 <output_collection name="output_collection" type="list"> 36 <output_collection name="output_collection" type="list">
45 <element name="missing_loci_stats"> 37 <element name="missing_loci_stats">
46 <assert_contents> 38 <assert_contents>
47 <has_text_matching expression="GCA_000007265"/> 39 <has_text_matching expression="GCA_000007265"/>
48 </assert_contents> 40 </assert_contents>