Mercurial > repos > devteam > picard_122_up
comparison picard_NormalizeFasta.xml @ 0:b76a4f17bbbb draft
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author | devteam |
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date | Thu, 23 Oct 2014 11:31:30 -0400 |
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-1:000000000000 | 0:b76a4f17bbbb |
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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}" "${fasta_file}" && | |
18 | |
19 java -jar \$JAVA_JAR_PATH/NormalizeFasta.jar | |
20 | |
21 INPUT="${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 |