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comparison VCF2Hapmap/vcf2FastaAndHapmap.xml @ 4:10627af23f10 draft

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planemo upload
author gandres
date Tue, 15 Dec 2015 05:18:02 -0500
parents 420b57c3c185
children
comparison
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3:345f88a8f483 4:10627af23f10
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements> 7 <requirements>
8 <requirement type="binary">perl</requirement> 8 <requirement type="binary">perl</requirement>
9 </requirements> 9 </requirements>
10 10
11 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
12 <stdio>
13 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
14 <exit_code range="1:" level="fatal" />
15 </stdio>
16
11 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> 17 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
12 <version_command> 18 <version_command>
13 <!-- 19 <!--
14 tool_binary -v 20 tool_binary -v
15 --> 21 -->
16 </version_command> 22 </version_command>
17 23
18 <!-- [REQUIRED] The command to execute --> 24 <!-- [REQUIRED] The command to execute -->
19 <command interpreter="bash"> 25 <command interpreter="bash">
20 vcf2FastaAndHapmap.sh $filein $fileout_label $fileout $optional.file_opt 26 vcf2FastaAndHapmap.sh $filein $fileout $optional.file_opt
21 #if str( $optional.file_opt ) != "none": 27 #if str( $optional.file_opt ) != "none":
22 $fileout_seq $fileout_fa1 $filefasta 28 $fileout_seq $fileout_fa1 $filefasta
23 #if str( $optional.file_opt ) == "fasta_gff": 29 #if str( $optional.file_opt ) == "fasta_gff":
24 $filegff 30 $filegff
25 #end if 31 #end if
56 <data name="fileout_fa1" format="fasta" label="${fileout_label}.gene_alignment.fas"> 62 <data name="fileout_fa1" format="fasta" label="${fileout_label}.gene_alignment.fas">
57 <filter>(optional['file_opt'] == 'fasta_gff')</filter> 63 <filter>(optional['file_opt'] == 'fasta_gff')</filter>
58 </data> 64 </data>
59 </outputs> 65 </outputs>
60 66
61 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
62 <stdio>
63 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
64 <exit_code range="1:" level="fatal" />
65 </stdio>
66
67 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> 67 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
68 <tests> 68 <tests>
69 <!-- [HELP] Test files have to be in the ~/test-data directory --> 69 <!-- [HELP] Test files have to be in the ~/test-data directory -->
70 <test> 70 <test>
71 <param name="filein" value="sample.vcf" /> 71 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
72 <param name="otpional.file_opt" value="none" /> 72 <param name="file_opt" value="none" />
73 <output name="fileout" file="result1.hapmap" /> 73 <output name="fileout" file="vcf2fastaAndHapmap-result1.hapmap" />
74 </test> 74 </test>
75 <test> 75 <test>
76 <param name="filein" value="sample.vcf" /> 76 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
77 <param name="otpional.file_opt" value="fasta" /> 77 <param name="file_opt" value="fasta" />
78 <param name="filefasta" value="reference.fa" /> 78 <param name="filefasta" value="vcf2fastaAndHapmap-reference.fa" />
79 <output name="fileout" file="result2.hapmap" /> 79 <output name="fileout" file="vcf2fastaAndHapmap-result2.hapmap" />
80 <output name="fileout_seq" file="result2.flanking.txt" /> 80 <output name="fileout_seq" file="vcf2fastaAndHapmap-result2.flanking.txt" />
81 <output name="fileout_fa1" file="result2.gene_alignment.fas" /> 81 </test>
82 <test>
83 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
84 <param name="file_opt" value="fasta_gff" />
85 <param name="filefasta" value="vcf2fastaAndHapmap-reference.fa" />
86 <param name="filegff" value="vcf2fastaAndHapmap-reference.gff" />
87 <output name="fileout" file="vcf2fastaAndHapmap-result3.hapmap" />
88 <output name="fileout_seq" file="vcf2fastaAndHapmap-result3.flanking.txt" />
89 <output name="fileout_fa1" file="vcf2fastaAndHapmap-result3.gene_alignment.fas" />
82 </test> 90 </test>
83 </tests> 91 </tests>
84 92
85 <!-- [OPTIONAL] Help displayed in Galaxy --> 93 <!-- [OPTIONAL] Help displayed in Galaxy -->
86 <help> 94 <help>