Mercurial > repos > dcouvin > countdifferences
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/countDifferences.xml Mon Sep 20 21:51:24 2021 +0000 @@ -0,0 +1,50 @@ +<tool id="countdifferences" name="countDifferences tool" version="1.0.0"> + <description>allows to compare sequences from a multi-Fasta alignment file by calculating differences (in bp) and percentage identity</description> + +<requirements> + <requirement type="package" version="1.7.2">perl-bioperl</requirement> + <!--<requirement type="package" version="3.27">perl-string-approx</requirement>--> +</requirements> + +<command detect_errors="aggressive"><![CDATA[ + +#import re + ## Creates symlinks for each input file based on the Galaxy 'element_identifier' + ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') + ## Add single quotes around each input file identifier + #set $_input_file = "'{}'".format($input.element_identifier) + ln -s '${input}' ${_input_file} && + + + perl '$__tool_directory__/countDifferences.pl' $_input_file $output1 $output2 + + + +]]></command> + <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output" --> + <!-- ./nuclescore.sh ${named_input_files} > "$output" --> + +<inputs> + <param format="fasta" name="input" type="data" label="Multi-FASTA file: "/> + <!--<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" />--> +</inputs> + + <outputs> + <data format="tabular" name="output1" label="bp_differences.tsv "/> + <data format="tabular" name="output2" label="percentage_identity.tsv "/> + </outputs> + +<help><![CDATA[ +countDifferences.pl is a Perl script allowing to calculate differences (changes in bp) and sequences percentage identity from an aligned multi-Fasta file. + +Two resulting tables are produced: +(i) a table containing a matrix with bp differences for each sequence; +(ii) a table containing a matrix with percentage identity for each sequence + +This script belongs to the getSequenceInfo supplementary tools. + +- GitHub: https://github.com/karubiotools/getSequenceInfo/tree/master/supplementary_tools +]]> +</help> + +</tool>