|
75
|
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="${__new_file_path__}"
|
|
|
20 </command>
|
|
|
21
|
|
|
22 <stdio>
|
|
|
23 <exit_code range="0" level="warning" description="Tool finished correctly" />
|
|
|
24 </stdio>
|
|
|
25
|
|
|
26 <inputs>
|
|
|
27 <param name="title" label="Name for the output fasta file" type="text" default="output" />
|
|
|
28 <param format="fasta" name="OUTPUT" type="data" label="The output fasta file to write. Required." help="" />
|
|
|
29 <param name="LINE_LENGTH" type="integer" label="The line length to be used for the output fasta file. Default value: 100. This option can be set to 'null' to clear the default value." help="" />
|
|
|
30 <param name="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE" type="boolean" label="Truncate sequence names at first whitespace. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
|
|
|
31 </inputs>
|
|
|
32 <outputs>
|
|
|
33 <data format="fasta" name="output1" label="${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>
|
