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comparison picard_NormalizeFasta.xml @ 5:3d4f1fa26f0e draft

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author devteam
date Tue, 16 Dec 2014 19:03:21 -0500
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4:ab1f60c26526 5:3d4f1fa26f0e
1 <tool name="NormalizeFasta" id="picard_NormalizeFasta" version="1.126.0">
2 <description>normalize fasta datasets</description>
3 <requirements>
4 <requirement type="package" version="1.126.0">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}" "${fasta_file}" &amp;&amp;
18
19 java -jar \$JAVA_JAR_PATH/picard.jar
20 NormalizeFasta
21
22 INPUT="${fasta_file}"
23 OUTPUT="${outFile}"
24 LINE_LENGTH="${line_length}"
25 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
26
27 QUIET=true
28 VERBOSITY=ERROR
29
30 </command>
31 <inputs>
32 <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" />
33 <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
34 <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
35 </inputs>
36
37 <outputs>
38 <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
39 </outputs>
40
41 <tests>
42 <test>
43 <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
44 <param name="line_length" value="40"/>
45 <param name="truncate_sequence_names_at_whitespaces" value="False"/>
46 <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
47 </test>
48 </tests>
49
50 <stdio>
51 <exit_code range="1:" level="fatal"/>
52 </stdio>
53
54 <help>
55
56 **Purpose**
57
58 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.
59
60 @dataset_collections@
61
62 @description@
63
64 LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100.
65
66 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean
67 Truncate sequence names at first whitespace. Default value: false. Possible values: {true, false}
68
69 @more_info@
70
71 </help>
72 </tool>
73
74