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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.</description>
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3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
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4 <command interpreter="bash">
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5 normalizefasta_wrapper.sh NormalizeFasta.jar
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6
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7 ${input}
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8 OUTPUT="${output1}"
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9 #if str( $LINE_LENGTH ):
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10 LINE_LENGTH="${LINE_LENGTH}"
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11 #end if
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12 #if str( $TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE ):
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13 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE}"
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14 #end if
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15
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16 VALIDATION_STRINGENCY=LENIENT
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17 QUIET=True
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18 TMP_DIR="${__new_file_path__}"
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19 </command>
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20
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21 <inputs>
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22 <param format="fasta" name="input" type="data" label="The input fasta file. Required." help="" />
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23 <param name="title" label="Name for the output fasta file" type="text" default="normalized_fasta" />
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24 <param name="LINE_LENGTH" type="integer" value="100" label="The line length to be used for the output fasta file. Default value: 100. This option can be set to 'null' to clear the default value." help="" />
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25 <param name="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE" type="boolean" label="Truncate sequence names at first whitespace. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
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26 </inputs>
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27 <outputs>
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28 <data format="fasta" name="output1" label="${title}.fasta" >
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29 </data>
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30 </outputs>
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31 <!-- <tests>
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32 <test> -->
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33 <!-- Here is a command line that works:
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34 java -jar ...
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35 -->
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36 <!-- <param name="inputFile" value="XXCHANGEMEE-input" />
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37 <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" />
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38 </test>
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39 </tests> -->
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40 <help>
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41 Picard documentation says:
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42
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43
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44 NormalizeFasta
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45
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46 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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47 Option Description
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48 INPUT=File The input fasta file to normalize. Required.
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49 OUTPUT=File The output fasta file to write. Required.
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50 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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51 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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52
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53
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54 </help>
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55 </tool>
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