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1 <tool name="NormalizeFasta" id="picard_NormalizeFasta" version="1.106.0">
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2 <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>
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3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
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4 <command interpreter="java -jar -Xmx8g">
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5 $JAVA_JAR_PATH/NormalizeFasta.jar
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6
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7 #if str( $OUTPUT ):
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8 OUTPUT="${OUTPUT}"
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9 #end if
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10 #if str( $LINE_LENGTH ):
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11 LINE_LENGTH="${LINE_LENGTH}"
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12 #end if
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13 #if str( $TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE ):
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14 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE}"
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15 #end if
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16
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17 VALIDATION_STRINGENCY=LENIENT
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18 QUIET=True
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19 TMP_DIR="${__new_file_path__}"
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20 </command>
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21
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22 <stdio>
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23 <exit_code range="0" level="warning" description="Tool finished correctly" />
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24 </stdio>
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25
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26 <inputs>
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27 <param format="XXCHANGEMEEE" name="OUTPUT" type="data" label="The output fasta file to write. Required." help="" />
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28 <param format="XXCHANGEMEEE" name="LINE_LENGTH" type="integer" 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="" />
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29 <param format="XXCHANGEMEEE" 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="" />
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30 </inputs>
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31 <outputs>
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32 <data name="outFile" format="XXCHANGEMEEE">
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33 </data>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <!-- Here is a command line that works:
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38 java -jar ...
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39 -->
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40 <param name="inputFile" value="XXCHANGEMEE-input" />
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41 <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" />
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42 </test>
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43 </tests>
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44 <help>
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45 Picard documentation says:
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46
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47
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48 NormalizeFasta
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49
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50 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.
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51 Option Description
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52 INPUT=File The input fasta file to normalize. Required.
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53 OUTPUT=File The output fasta file to write. Required.
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54 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.
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55 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}
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56
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57
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58 </help>
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59 </tool>
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