Mercurial > repos > dcouvin > countdifferences
comparison countDifferences.xml @ 0:a9fb5e4abb2d draft default tip
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author | dcouvin |
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date | Mon, 20 Sep 2021 21:51:24 +0000 |
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-1:000000000000 | 0:a9fb5e4abb2d |
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1 <tool id="countdifferences" name="countDifferences tool" version="1.0.0"> | |
2 <description>allows to compare sequences from a multi-Fasta alignment file by calculating differences (in bp) and percentage identity</description> | |
3 | |
4 <requirements> | |
5 <requirement type="package" version="1.7.2">perl-bioperl</requirement> | |
6 <!--<requirement type="package" version="3.27">perl-string-approx</requirement>--> | |
7 </requirements> | |
8 | |
9 <command detect_errors="aggressive"><![CDATA[ | |
10 | |
11 #import re | |
12 ## Creates symlinks for each input file based on the Galaxy 'element_identifier' | |
13 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') | |
14 ## Add single quotes around each input file identifier | |
15 #set $_input_file = "'{}'".format($input.element_identifier) | |
16 ln -s '${input}' ${_input_file} && | |
17 | |
18 | |
19 perl '$__tool_directory__/countDifferences.pl' $_input_file $output1 $output2 | |
20 | |
21 | |
22 | |
23 ]]></command> | |
24 <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output" --> | |
25 <!-- ./nuclescore.sh ${named_input_files} > "$output" --> | |
26 | |
27 <inputs> | |
28 <param format="fasta" name="input" type="data" label="Multi-FASTA file: "/> | |
29 <!--<param name="char" type="text" area="false" value="N" label="Character to be removed from Multi-FASTA file:" help="Users can directly write the character to be removed without quotes" />--> | |
30 </inputs> | |
31 | |
32 <outputs> | |
33 <data format="tabular" name="output1" label="bp_differences.tsv "/> | |
34 <data format="tabular" name="output2" label="percentage_identity.tsv "/> | |
35 </outputs> | |
36 | |
37 <help><![CDATA[ | |
38 countDifferences.pl is a Perl script allowing to calculate differences (changes in bp) and sequences percentage identity from an aligned multi-Fasta file. | |
39 | |
40 Two resulting tables are produced: | |
41 (i) a table containing a matrix with bp differences for each sequence; | |
42 (ii) a table containing a matrix with percentage identity for each sequence | |
43 | |
44 This script belongs to the getSequenceInfo supplementary tools. | |
45 | |
46 - GitHub: https://github.com/karubiotools/getSequenceInfo/tree/master/supplementary_tools | |
47 ]]> | |
48 </help> | |
49 | |
50 </tool> |