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comparison picard_NormalizeFasta.xml @ 0:b76a4f17bbbb draft

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author devteam
date Thu, 23 Oct 2014 11:31:30 -0400
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1 <tool name="NormalizeFasta" id="picard_NormalizeFasta" version="1.122.0">
2 <description>normalize fasta datasets</description>
3 <requirements>
4 <requirement type="package" version="1.122.0">picard</requirement>
5 </requirements>
6
7 <macros>
8 <import>picard_macros.xml</import>
9 </macros>
10
11 <command>
12 @java_options@
13
14
15 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
16 #set $fasta_file="local_fasta.fa"
17 ln -s "${inputFile}" "${fasta_file}" &amp;&amp;
18
19 java -jar \$JAVA_JAR_PATH/NormalizeFasta.jar
20
21 INPUT="${fasta_file}"
22 OUTPUT="${outFile}"
23 LINE_LENGTH="${line_length}"
24 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
25
26 QUIET=true
27 VERBOSITY=ERROR
28
29 </command>
30 <inputs>
31 <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" />
32 <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
33 <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
34 </inputs>
35
36 <outputs>
37 <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
38 </outputs>
39
40 <tests>
41 <test>
42 <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
43 <param name="line_length" value="40"/>
44 <param name="truncate_sequence_names_at_whitespaces" value="False"/>
45 <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
46 </test>
47 </tests>
48
49 <stdio>
50 <exit_code range="1:" level="fatal"/>
51 </stdio>
52
53 <help>
54
55 **Purpose**
56
57 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.
58
59 @dataset_collections@
60
61 @description@
62
63 LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100.
64
65 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean
66 Truncate sequence names at first whitespace. Default value: false. Possible values: {true, false}
67
68 @more_info@
69
70 </help>
71 </tool>
72
73