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comparison picard_NormalizeFasta.xml @ 92:29447daa90e0 draft

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author devteam
date Mon, 24 Feb 2014 00:42:27 -0500
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91:2abf873fdbf8 92:29447daa90e0
1 <tool name="NormalizeFasta" id="picard_NormalizeFasta" version="1.106.0">
2 <description>Takes any file that conforms to the fasta format and normalizes it.</description>
3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
4 <command interpreter="bash">
5 normalizefasta_wrapper.sh NormalizeFasta.jar
6
7 ${input}
8 OUTPUT="${output1}"
9 #if str( $LINE_LENGTH ):
10 LINE_LENGTH="${LINE_LENGTH}"
11 #end if
12 #if str( $TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE ):
13 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE}"
14 #end if
15
16 VALIDATION_STRINGENCY=LENIENT
17 QUIET=True
18 TMP_DIR="${__new_file_path__}"
19 </command>
20
21 <inputs>
22 <param format="fasta" name="input" type="data" label="The input fasta file. Required." help="" />
23 <param name="title" label="Name for the output fasta file" type="text" default="normalized_fasta" />
24 <param name="LINE_LENGTH" type="integer" value="100" label="The line length to be used for the output fasta file. Default value: 100. This option can be set to 'null' to clear the default value." help="" />
25 <param name="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE" type="boolean" label="Truncate sequence names at first whitespace. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
26 </inputs>
27 <outputs>
28 <data format="fasta" name="output1" label="${title}.fasta" >
29 </data>
30 </outputs>
31 <!-- <tests>
32 <test> -->
33 <!-- Here is a command line that works:
34 java -jar ...
35 -->
36 <!-- <param name="inputFile" value="XXCHANGEMEE-input" />
37 <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" />
38 </test>
39 </tests> -->
40 <help>
41 Picard documentation says:
42
43
44 NormalizeFasta
45
46 Takes any file 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.
47 Option Description
48 INPUT=File The input fasta file to normalize. Required.
49 OUTPUT=File The output fasta file to write. Required.
50 LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100. This option can be set to 'null' to clear the default value.
51 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean Truncate sequence names at first whitespace. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
52
53
54 </help>
55 </tool>