|
0
|
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
|
|
6
|
23 perl ${__tool_directory__}/PGAP_wrapper2.pl -g $input_files -p $proteins -l $named_input_files -o $output >>$logfile 2>&1
|
|
0
|
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"/>
|
|
6
|
35 <data format="txt" name="logfile" label="Logfile"/>
|
|
0
|
36 </outputs>
|
|
|
37
|
|
|
38 </tool>
|
