view picard_NormalizeFasta.xml @ 77:3115e34e348f draft

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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 so that all lines of sequence except the last line per named sequence are of the same length.</description>
<requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
  <command interpreter="java -jar -Xmx8g">
      $JAVA_JAR_PATH/NormalizeFasta.jar

          #if str( $OUTPUT ):
              OUTPUT="${OUTPUT}"
          #end if
          #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>
  
  <stdio>
    <exit_code range="0" level="warning" description="Tool finished correctly" />
  </stdio>
  
  <inputs>
       <param name="title" label="Name for the output fasta file" type="text" default="output" />
      <param format="fasta" name="OUTPUT" type="data" label="The output fasta file to write. Required." help="" />
      <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>