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comparison picard_NormalizeFasta.xml @ 7:08f69add4d06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:36 -0500
parents 52fdfc45590a
children e417b1d6288d
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6:961236c5ec73 7:08f69add4d06
2 <description>normalize fasta datasets</description> 2 <description>normalize fasta datasets</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command> 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 9
10 10
11 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa 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" 12 #set $fasta_file="local_fasta.fa"
13 ln -s "${inputFile}" "${fasta_file}" &amp;&amp; 13 ln -s "${inputFile}" "${fasta_file}" &&
14 14
15 java -jar \$JAVA_JAR_PATH/picard.jar 15 picard
16 NormalizeFasta 16 NormalizeFasta
17 17
18 INPUT="${fasta_file}" 18 INPUT="${fasta_file}"
19 OUTPUT="${outFile}" 19 OUTPUT="${outFile}"
20 LINE_LENGTH="${line_length}" 20 LINE_LENGTH="${line_length}"
21 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}" 21 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
22 22
23 QUIET=true 23 QUIET=true
24 VERBOSITY=ERROR 24 VERBOSITY=ERROR
25 25
26 </command> 26 ]]></command>
27 <inputs> 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" /> 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"/> 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"/> 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> 31 </inputs>
41 <param name="truncate_sequence_names_at_whitespaces" value="False"/> 41 <param name="truncate_sequence_names_at_whitespaces" value="False"/>
42 <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/> 42 <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
43 </test> 43 </test>
44 </tests> 44 </tests>
45 45
46 <stdio>
47 <exit_code range="1:" level="fatal"/>
48 </stdio>
49 46
50 <help> 47 <help>
51 48
52 **Purpose** 49 **Purpose**
53 50