annotate PGAP.xml @ 6:c43a55b28d06 draft

Uploaded
author dereeper
date Fri, 25 Jun 2021 16:25:53 +0000
parents d8c5bea1cce2
children 86de4251345f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
1 <tool id="PGAP" name="PGAP" version="1.0">
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
2 <description>Pan-Genome Analysis Pipeline </description>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
3 <requirements>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
4 <requirement type="package" version="2.11.0">blast</requirement>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
5 <requirement type="package" version="7.480">mafft</requirement>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
6 <requirement type="package" version="14.137">mcl</requirement>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
7 <requirement type="package" version="3.697">phylip</requirement>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
8 <requirement type="package" version="1.7.2">perl-bioperl</requirement>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
9 </requirements> -->
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
10 <command detect_errors="aggressive"><![CDATA[
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
11 #import re
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
12
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
13 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
14 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
15 #set $named_input_files = ''
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
16 #for $input_file in $input_files
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
17 ## Add single quotes around each input file identifier
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
18 #set $_input_file = "'{}'".format($input_file.element_identifier)
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
19 ln -s '${input_file}' ${_input_file} &&
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
20 #set $named_input_files = $named_input_files + ',' + $_input_file
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
21 #end for
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
22
6
c43a55b28d06 Uploaded
dereeper
parents: 5
diff changeset
23 perl ${__tool_directory__}/PGAP_wrapper2.pl -g $input_files -p $proteins -l $named_input_files -o $output >>$logfile 2>&1
0
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
24 ]]></command>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
25
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
26
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
27
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
28 <inputs>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
29 <param format="fasta" name="input_files" type="data" multiple="true" label="Coding genes FASTA files"/>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
30 <param format="fasta" name="proteins" type="data" multiple="true" label="Protein FASTA files"/>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
31 </inputs>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
32
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
33 <outputs>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
34 <data format="txt" name="output" label="Pangenome presence absence matrix"/>
6
c43a55b28d06 Uploaded
dereeper
parents: 5
diff changeset
35 <data format="txt" name="logfile" label="Logfile"/>
0
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
36 </outputs>
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
37
83e62a1aeeeb Uploaded
dereeper
parents:
diff changeset
38 </tool>