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view picard_NormalizeFasta.xml @ 131:3321bce585e5 draft
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author | devteam |
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date | Wed, 26 Feb 2014 02:11:06 -0500 |
parents | 29447daa90e0 |
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<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="1.106.0"> <description>Takes any file that conforms to the fasta format and normalizes it.</description> <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements> <command interpreter="bash"> normalizefasta_wrapper.sh NormalizeFasta.jar ${input} OUTPUT="${output1}" #if str( $LINE_LENGTH ): LINE_LENGTH="${LINE_LENGTH}" #end if #if str( $TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE ): TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE}" #end if VALIDATION_STRINGENCY=LENIENT QUIET=True TMP_DIR="${__new_file_path__}" </command> <inputs> <param format="fasta" name="input" type="data" label="The input fasta file. Required." help="" /> <param name="title" label="Name for the output fasta file" type="text" default="normalized_fasta" /> <param name="LINE_LENGTH" type="integer" value="100" label="The line length to be used for the output fasta file. Default value: 100. This option can be set to 'null' to clear the default value." help="" /> <param name="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE" type="boolean" label="Truncate sequence names at first whitespace. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" /> </inputs> <outputs> <data format="fasta" name="output1" label="${title}.fasta" > </data> </outputs> <!-- <tests> <test> --> <!-- Here is a command line that works: java -jar ... --> <!-- <param name="inputFile" value="XXCHANGEMEE-input" /> <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" /> </test> </tests> --> <help> Picard documentation says: NormalizeFasta Takes any file 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. Option Description INPUT=File The input fasta file to normalize. Required. OUTPUT=File The output fasta file to write. Required. LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100. This option can be set to 'null' to clear the default value. TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean Truncate sequence names at first whitespace. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} </help> </tool>