Mercurial > repos > dcouvin > nuclescore
comparison nuclescore.xml @ 0:82dce1eb9074 draft default tip
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author | dcouvin |
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date | Fri, 03 Sep 2021 22:36:56 +0000 |
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-1:000000000000 | 0:82dce1eb9074 |
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1 <tool id="nuclescore" name="NucleScore tool" version="0.1.0"> | |
2 <description>allows to get information for classification of genome assemblies</description> | |
3 | |
4 <requirements> | |
5 <requirement type="package" version="1.7.2">perl-bioperl</requirement> | |
6 </requirements> | |
7 | |
8 <command detect_errors="aggressive"><![CDATA[ | |
9 | |
10 #import re | |
11 ## Creates symlinks for each input file based on the Galaxy 'element_identifier' | |
12 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') | |
13 #set $named_input_files = '' | |
14 #for $input_file in $input_files | |
15 ## Add single quotes around each input file identifier | |
16 #set $_input_file = "'{}'".format($input_file.element_identifier) | |
17 ln -s '${input_file}' ${_input_file} && | |
18 #set $named_input_files = $named_input_files + ' ' + $_input_file | |
19 #end for | |
20 | |
21 | |
22 perl '$__tool_directory__/nucleScore.pl' $named_input_files > "$output" | |
23 | |
24 | |
25 | |
26 ]]></command> | |
27 <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output" --> | |
28 <!-- ./nuclescore.sh ${named_input_files} > "$output" --> | |
29 | |
30 <inputs> | |
31 <param format="fasta" name="input_files" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/> | |
32 </inputs> | |
33 | |
34 <outputs> | |
35 <data format="tabular" name="output" /> | |
36 </outputs> | |
37 | |
38 <help><![CDATA[ | |
39 nucleScore.pl is a Perl script allowing to get information for classification of genome assemblies basing on nucleotides data (GC percent, AT/GC ratio, ...) | |
40 | |
41 This script belongs to the getSequenceInfo supplementary tools | |
42 | |
43 - GitHub: https://github.com/karubiotools/getSequenceInfo/tree/master/supplementary_tools | |
44 ]]> | |
45 </help> | |
46 | |
47 </tool> |