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comparison picard_NormalizeFasta.xml @ 0:5166ed57b1c4 draft

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Uploaded version 1.135
author avowinkel
date Mon, 06 Jul 2015 14:46:32 -0400
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-1:000000000000 0:5166ed57b1c4
1 <tool name="NormalizeFasta" id="picard_NormalizeFasta" version="1.135">
2 <description>normalize fasta datasets</description>
3 <macros>
4 <import>picard_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>
8 @java_options@
9
10
11 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
12 #set $fasta_file="local_fasta.fa"
13 ln -s "${inputFile}" "${fasta_file}" &amp;&amp;
14
15 java -jar \$JAVA_JAR_PATH/picard.jar
16 NormalizeFasta
17
18 INPUT="${fasta_file}"
19 OUTPUT="${outFile}"
20 LINE_LENGTH="${line_length}"
21 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
22
23 QUIET=true
24 VERBOSITY=ERROR
25
26 </command>
27 <inputs>
28 <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" />
29 <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
30 <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
31 </inputs>
32
33 <outputs>
34 <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
35 </outputs>
36
37 <tests>
38 <test>
39 <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
40 <param name="line_length" value="40"/>
41 <param name="truncate_sequence_names_at_whitespaces" value="False"/>
42 <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
43 </test>
44 </tests>
45
46 <stdio>
47 <exit_code range="1:" level="fatal"/>
48 </stdio>
49
50 <help>
51
52 **Purpose**
53
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.
55
56 @dataset_collections@
57
58 @description@
59
60 LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100.
61
62 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean
63 Truncate sequence names at first whitespace. Default value: false. Possible values: {true, false}
64
65 @more_info@
66
67 </help>
68 </tool>
69
70