Mercurial > repos > devteam > picard
view picard_NormalizeFasta.xml @ 10:777ccdd1d6e4 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author | devteam |
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date | Sun, 11 Oct 2015 10:46:17 -0400 |
parents | 3a3234d7a2e8 |
children | 05087b27692a |
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<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.0"> <description>normalize fasta datasets</description> <macros> <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> <command> @java_options@ ## Two lines below are due to the fact that picard likes fasta files to have extension .fa #set $fasta_file="local_fasta.fa" ln -s "${inputFile}" "${fasta_file}" && java -jar \$JAVA_JAR_PATH/picard.jar NormalizeFasta INPUT="${fasta_file}" OUTPUT="${outFile}" LINE_LENGTH="${line_length}" TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}" QUIET=true VERBOSITY=ERROR </command> <inputs> <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" /> <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/> <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/> </inputs> <outputs> <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/> </outputs> <tests> <test> <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/> <param name="line_length" value="40"/> <param name="truncate_sequence_names_at_whitespaces" value="False"/> <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/> </test> </tests> <stdio> <exit_code range="1:" level="fatal"/> </stdio> <help> **Purpose** Takes any dataset that conforms to the fasta format and normalizes it so that all lines of sequence except the last line per named sequence are of the same length. @dataset_collections@ @description@ LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100. TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean Truncate sequence names at first whitespace. Default value: false. Possible values: {true, false} @more_info@ </help> </tool>