Mercurial > repos > mgarnier > catchsequence
comparison catchsequence/catchsequence.xml @ 0:c30eb2050ef5 draft default tip
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author | mgarnier |
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date | Thu, 26 Aug 2021 13:41:33 +0000 |
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-1:000000000000 | 0:c30eb2050ef5 |
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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> |