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annotate picard_NormalizeFasta.xml @ 10:126c30841c38 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
author devteam
date Thu, 08 Dec 2016 06:43:24 -0500
parents 41b8d087a2d2
children 486d7500da69
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.0">
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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 detect_errors="exit_code"><![CDATA[
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8 @java_options@
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10 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
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11 #import re
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12 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
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13 ln -f -s '$inputFile' '$escaped_element_identifier'.fa &&
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14 picard
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15 NormalizeFasta
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17 INPUT='$escaped_element_identifier'.fa
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18 OUTPUT="${outFile}"
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19 LINE_LENGTH="${line_length}"
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20 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
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22 QUIET=true
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23 VERBOSITY=ERROR
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25 ]]></command>
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26 <inputs>
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27 <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" />
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28 <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
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29 <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
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30 </inputs>
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32 <outputs>
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33 <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
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34 </outputs>
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36 <tests>
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37 <test>
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38 <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
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39 <param name="line_length" value="40"/>
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40 <param name="truncate_sequence_names_at_whitespaces" value="False"/>
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41 <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
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42 </test>
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43 </tests>
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46 <help>
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48 **Purpose**
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50 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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52 @dataset_collections@
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54 @description@
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56 LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100.
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58 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean
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59 Truncate sequence names at first whitespace. Default value: false. Possible values: {true, false}
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61 @more_info@
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63 </help>
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64 </tool>
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