Mercurial > repos > devteam > vcfvcfintersect
comparison vcfvcfintersect.xml @ 5:c2026da116b4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
author | iuc |
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date | Mon, 26 Mar 2018 12:16:48 -0400 |
parents | 64d95a7df265 |
children | 46fde0ec9efa |
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4:64d95a7df265 | 5:c2026da116b4 |
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1 <tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="@WRAPPER_VERSION@.0"> | 1 <tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="@WRAPPER_VERSION@+galaxy0"> |
2 <description>Intersect two VCF datasets</description> | 2 <description>Intersect two VCF datasets</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
58 </param> | 58 </param> |
59 <when value="no" /> | 59 <when value="no" /> |
60 <when value="use_adv_controls"> | 60 <when value="use_adv_controls"> |
61 <param name="adv_options_input" type="text" value="-t "vcfvcf-intersect-result"" | 61 <param name="adv_options_input" type="text" value="-t "vcfvcf-intersect-result"" |
62 label="Enter additional command line options described in the help section below" | 62 label="Enter additional command line options described in the help section below" |
63 help="such as -m, -t, -V, -M, and -T" /> | 63 help="such as -m, -t, -V, -M, and -T"> |
64 <sanitizer> | 64 <sanitizer> |
65 <valid initial="string.printable"> | 65 <valid initial="string.printable"> |
66 <remove value="'"/> | 66 <remove value="'"/> |
67 </valid> | 67 </valid> |
68 <mapping initial="none"> | 68 <mapping initial="none"> |
69 <add source="'" target="__sq__"/> | 69 <add source="'" target="__sq__"/> |
70 </mapping> | 70 </mapping> |
71 </sanitizer> | 71 </sanitizer> |
72 </param> | |
72 </when> | 73 </when> |
73 </conditional> | 74 </conditional> |
74 </inputs> | 75 </inputs> |
75 <outputs> | 76 <outputs> |
76 <data format="vcf" name="out_file1" /> | 77 <data format="vcf" name="out_file1" /> |
82 <param name="reference_source_selector" value="history" /> | 83 <param name="reference_source_selector" value="history" /> |
83 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> | 84 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> |
84 <param name="isect_union" value="-i" /> | 85 <param name="isect_union" value="-i" /> |
85 <param name="invert" value="False" /> | 86 <param name="invert" value="False" /> |
86 <param name="loci" value="False" /> | 87 <param name="loci" value="False" /> |
87 <patam name="adv_options_selector" value="no" /> | 88 <param name="adv_options_selector" value="no" /> |
88 <param name="window_size" value="30" /> | 89 <param name="window_size" value="30" /> |
89 <output name="out_file1" file="vcfvcfintersect-test1.vcf"/> | 90 <output name="out_file1" file="vcfvcfintersect-test1.vcf"/> |
90 </test> | 91 </test> |
91 <test> | 92 <test> |
92 <param name="reference_source_selector" value="history" /> | 93 <param name="reference_source_selector" value="history" /> |
93 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> | 94 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> |
94 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> | 95 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> |
95 <param name="isect_union" value="-u" /> | 96 <param name="isect_union" value="-u" /> |
96 <param name="invert" value="False" /> | 97 <param name="invert" value="False" /> |
97 <param name="loci" value="False" /> | 98 <param name="loci" value="False" /> |
98 <patam name="adv_options_selector" value="no" /> | 99 <param name="adv_options_selector" value="no" /> |
99 <param name="window_size" value="30" /> | 100 <param name="window_size" value="30" /> |
100 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> | 101 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> |
101 <output name="out_file1" file="vcfvcfintersect-test2.vcf"/> | 102 <output name="out_file1" file="vcfvcfintersect-test2.vcf"/> |
102 </test> | 103 </test> |
103 </tests> | 104 </tests> |