Mercurial > repos > dcouvin > concatenatemultifasta
view concatenateMultiFasta.xml @ 0:640361a4d2ef draft default tip
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author | dcouvin |
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date | Fri, 17 Sep 2021 19:23:57 +0000 |
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<tool id="concatenatemultifasta" name="concatenateMultiFasta tool" version="0.1.0"> <description>allows to concatenate sequences from a multi-Fasta file</description> <!--<requirements> <requirement type="package" version="1.7.2">perl-bioperl</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__/concatenateMultiFasta.pl' $_input_file > "$output" ]]></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: "/> </inputs> <outputs> <data format="fasta" name="output" /> </outputs> <help><![CDATA[ concatenateMultiFasta.pl is a Perl script allowing to concatenate/merge multi-Fasta files. Every Fasta sequences contained in one file will be concatenated and the output is a Fasta file containing a unique sequence. This script belongs to the getSequenceInfo supplementary tools. - GitHub: https://github.com/karubiotools/getSequenceInfo/tree/master/supplementary_tools ]]> </help> </tool>