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1 <tool name="NormalizeFasta" id="picard_NormalizeFasta" version="1.135">
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2 <description>normalize fasta datasets</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command>
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8 @java_options@
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9
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10
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11 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
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12 #set $fasta_file="local_fasta.fa"
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13 ln -s "${inputFile}" "${fasta_file}" &&
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14
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15 java -jar \$JAVA_JAR_PATH/picard.jar
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16 NormalizeFasta
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17
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18 INPUT="${fasta_file}"
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19 OUTPUT="${outFile}"
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20 LINE_LENGTH="${line_length}"
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21 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
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22
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23 QUIET=true
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24 VERBOSITY=ERROR
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25
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26 </command>
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27 <inputs>
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28 <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" />
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29 <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
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30 <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
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31 </inputs>
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32
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33 <outputs>
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34 <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
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35 </outputs>
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36
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37 <tests>
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38 <test>
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39 <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
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40 <param name="line_length" value="40"/>
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41 <param name="truncate_sequence_names_at_whitespaces" value="False"/>
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42 <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
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43 </test>
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44 </tests>
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45
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46 <stdio>
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47 <exit_code range="1:" level="fatal"/>
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48 </stdio>
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49
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50 <help>
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51
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52 **Purpose**
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53
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54 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.
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55
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56 @dataset_collections@
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57
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58 @description@
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59
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60 LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100.
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61
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62 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean
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63 Truncate sequence names at first whitespace. Default value: false. Possible values: {true, false}
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64
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65 @more_info@
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66
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67 </help>
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68 </tool>
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69
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70
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