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comparison picard_NormalizeFasta.xml @ 77:3115e34e348f draft

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author devteam
date Wed, 19 Feb 2014 23:10:37 -0500
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76:616de30c7afe 77:3115e34e348f
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 so that all lines of sequence except the last line per named sequence are of the same length.</description>
3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
4 <command interpreter="java -jar -Xmx8g">
5 $JAVA_JAR_PATH/NormalizeFasta.jar
6
7 #if str( $OUTPUT ):
8 OUTPUT="${OUTPUT}"
9 #end if
10 #if str( $LINE_LENGTH ):
11 LINE_LENGTH="${LINE_LENGTH}"
12 #end if
13 #if str( $TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE ):
14 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE}"
15 #end if
16
17 VALIDATION_STRINGENCY=LENIENT
18 QUIET=True
19 TMP_DIR="${__new_file_path__}"
20 </command>
21
22 <stdio>
23 <exit_code range="0" level="warning" description="Tool finished correctly" />
24 </stdio>
25
26 <inputs>
27 <param name="title" label="Name for the output fasta file" type="text" default="output" />
28 <param format="fasta" name="OUTPUT" type="data" label="The output fasta file to write. Required." help="" />
29 <param name="LINE_LENGTH" type="integer" value="100" label="The line length to be used for the output fasta file. Default value: 100. This option can be set to 'null' to clear the default value." help="" />
30 <param name="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE" type="boolean" label="Truncate sequence names at first whitespace. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
31 </inputs>
32 <outputs>
33 <data format="fasta" name="output1" label="${title}.fasta" >
34 </data>
35 </outputs>
36 <!-- <tests>
37 <test> -->
38 <!-- Here is a command line that works:
39 java -jar ...
40 -->
41 <!-- <param name="inputFile" value="XXCHANGEMEE-input" />
42 <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" />
43 </test>
44 </tests> -->
45 <help>
46 Picard documentation says:
47
48
49 NormalizeFasta
50
51 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.
52 Option Description
53 INPUT=File The input fasta file to normalize. Required.
54 OUTPUT=File The output fasta file to write. Required.
55 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.
56 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}
57
58
59 </help>
60 </tool>