Mercurial > repos > dereeper > pgap

comparison PGAP.xml @ 0:83e62a1aeeeb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dereeper
date Thu, 24 Jun 2021 13:51:52 +0000
parents
children 041355b97140
comparison
equal deleted inserted replaced
-1:000000000000 0:83e62a1aeeeb
1 <tool id="PGAP" name="PGAP" version="1.0">
2 <description>Pan-Genome Analysis Pipeline </description>
3 <requirements>
4 <requirement type="package" version="2.11.0">blast</requirement>
5 <requirement type="package" version="7.480">mafft</requirement>
6 <requirement type="package" version="14.137">mcl</requirement>
7 <requirement type="package" version="3.697">phylip</requirement>
8 <requirement type="package" version="1.7.2">perl-bioperl</requirement>
9 </requirements> -->
10 <command detect_errors="aggressive"><![CDATA[
11 #import re
12
13 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
14 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
15 #set $named_input_files = ''
16 #for $input_file in $input_files
17 ## Add single quotes around each input file identifier
18 #set $_input_file = "'{}'".format($input_file.element_identifier)
19 ln -s '${input_file}' ${_input_file} &&
20 #set $named_input_files = $named_input_files + ',' + $_input_file
21 #end for
22
23 perl ${__tool_directory__}/PGAP_wrapper2.pl -g $input_files -p $proteins -o $named_input_files -o $output
24 ]]></command>
25
26
27
28 <inputs>
29 <param format="fasta" name="input_files" type="data" multiple="true" label="Coding genes FASTA files"/>
30 <param format="fasta" name="proteins" type="data" multiple="true" label="Protein FASTA files"/>
31 </inputs>
32
33 <outputs>
34 <data format="txt" name="output" label="Pangenome presence absence matrix"/>
35
36 </outputs>
37
38 </tool>