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author mgarnier
date Thu, 26 Aug 2021 13:41:33 +0000
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1 <tool id="catchsequence" name="Catch Sequence" version="0.1.0">
2 <description>Catch sequence for BioloMICS import</description>
3 <requirements>
4 <requirement type="package" version="1.0.1">abricate</requirement>
5 <requirement type="package" version="2.19.0">mlst</requirement>
6 <!--<requirement type="package" version="6.6.0">emboss</requirement>
7 <requirement type="package" version="1.3.2">pandas</requirement>-->
8 </requirements>
9
10
11 <command detect_errors="aggressive"><![CDATA[
12
13 #import re
14 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
15 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
16 #set $named_input_files = ''
17 #for $input_file in $input_files
18 ## Add single quotes around each input file identifier
19 #set $_input_file = "'{}'".format($input_file.element_identifier)
20 ln -s '${input_file}' ${_input_file} &&
21 #set $named_input_files = $named_input_files + ' ' + $_input_file
22 #end for
23
24
25 perl '$__tool_directory__/catchsequence.pl' $named_input_files > "$output"
26
27
28
29 ]]></command>
30 <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output" -->
31 <!-- ./nuclescore.sh ${named_input_files} > "$output" -->
32
33 <inputs>
34 <param type="data" name="input_files" format="fasta" multiple="true" label="Genome fasta files"/>
35 <!-- <param format="fasta" name="input_files" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/> -->
36 </inputs>
37
38 <outputs>
39 <data format="tabular" name="output" />
40 </outputs>
41
42 <help>
43 No documentation
44 </help>
45
46 </tool>