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comparison picard_NormalizeFasta.xml @ 13:7e6fd3d0f16e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
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equal deleted inserted replaced
12:05087b27692a 13:7e6fd3d0f16e
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 detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 9
10 10 ## 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 11 ln -s '$inputFile' '$inputFile.element_identifier'.fa &&
12 #set $fasta_file="local_fasta.fa" 12
13 ln -s "${inputFile}" "${fasta_file}" &&
14
15 picard 13 picard
16 NormalizeFasta 14 NormalizeFasta
17 15
18 INPUT="${fasta_file}" 16 INPUT='$inputFile.element_identifier'.fa
19 OUTPUT="${outFile}" 17 OUTPUT="${outFile}"
20 LINE_LENGTH="${line_length}" 18 LINE_LENGTH="${line_length}"
21 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}" 19 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
22 20
23 QUIET=true 21 QUIET=true
24 VERBOSITY=ERROR 22 VERBOSITY=ERROR
25 23
26 ]]></command> 24 ]]></command>
27 <inputs> 25 <inputs>
28 <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" /> 26 <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" />
29 <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/> 27 <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
30 <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/> 28 <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
31 </inputs> 29 </inputs>
32 30
33 <outputs> 31 <outputs>
34 <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/> 32 <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
35 </outputs> 33 </outputs>
36 34
37 <tests> 35 <tests>
38 <test> 36 <test>
39 <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/> 37 <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
40 <param name="line_length" value="40"/> 38 <param name="line_length" value="40"/>
41 <param name="truncate_sequence_names_at_whitespaces" value="False"/> 39 <param name="truncate_sequence_names_at_whitespaces" value="False"/>
42 <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/> 40 <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
43 </test> 41 </test>
44 </tests> 42 </tests>
45 43
46 44
47 <help> 45 <help>
48 46
49 **Purpose** 47 **Purpose**
50 48
51 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. 49 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.
52 50
53 @dataset_collections@ 51 @dataset_collections@
54 52
55 @description@ 53 @description@
56 54
57 LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100. 55 LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100.
58 56
59 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean 57 TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean
60 Truncate sequence names at first whitespace. Default value: false. Possible values: {true, false} 58 Truncate sequence names at first whitespace. Default value: false. Possible values: {true, false}
61 59
62 @more_info@ 60 @more_info@
63 61
64 </help> 62 </help>
65 </tool> 63 </tool>