annotate 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
date Mon, 26 Mar 2018 12:16:48 -0400
parents 64d95a7df265
children 46fde0ec9efa
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
1 <tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="@WRAPPER_VERSION@+galaxy0">
4
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
2 <description>Intersect two VCF datasets</description>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
3 <macros>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
4 <import>macros.xml</import>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
5 </macros>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
6 <expand macro="requirements"/>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
7 <expand macro="stdio" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
8 <command>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
9 #set $reference_fasta_filename = "localref.fa"
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
10 #if str( $reference_source.reference_source_selector ) == "history":
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
11 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
12 #else:
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
14 #end if
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
15
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
16 #if $adv_options.adv_options_selector == "use_adv_controls":
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
17 vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}"
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
18 #else:
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
19 vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}"
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
20 #end if
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
21 </command>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
22 <inputs>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
23 <!-- selecting refernce source -->
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
24 <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
25 <param name="vcf_input2" type="data" format="vcf" label="The second VCF dataset"
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
26 help="The second dataset will be instersected with the first"/>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
27 <conditional name="reference_source">
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
28 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
29 help="This tools needs to access reference genomes sequence specified by this option.">
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
30 <option value="cached">Locally cached</option>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
31 <option value="history">History</option>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
32 </param>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
33 <when value="cached">
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
34 <param name="ref_file" type="select" label="Select reference genome">
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
35 <options from_data_table="fasta_indexes">
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
36 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
37 </options>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
38 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
39 </param>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
40 </when>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
41 <when value="history"> <!-- FIX ME!!!! -->
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
42 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
43 </when>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
44 </conditional>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
45 <param name="isect_union" type="select" label="Union or intersection" help="-i or -u">
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
46 <option value="-i">Intersect</option>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
47 <option value="-u">Union</option>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
48 </param>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
49 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
50 <param name="window_size" type="integer" value="30"
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
51 label="compare records up to this many bp away (window size)" help="-w, --window-size" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
52 <param name="loci" type="boolean" truevalue="-l" falsevalue=""
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
53 label="output whole loci when one alternate allele matches" help="-l, --loci" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
54 <conditional name="adv_options">
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
55 <param name="adv_options_selector" type="select" label="Advanced controls" help="Allows you to specify options that are not listed above">
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
56 <option value="no">Don't use advanced options</option>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
57 <option value="use_adv_controls">Use advanced options</option>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
58 </param>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
59 <when value="no" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
60 <when value="use_adv_controls">
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
61 <param name="adv_options_input" type="text" value="-t &quot;vcfvcf-intersect-result&quot;"
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
62 label="Enter additional command line options described in the help section below"
5
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
63 help="such as -m, -t, -V, -M, and -T">
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
64 <sanitizer>
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
65 <valid initial="string.printable">
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
66 <remove value="&apos;"/>
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
67 </valid>
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
68 <mapping initial="none">
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
69 <add source="&apos;" target="__sq__"/>
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
70 </mapping>
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
71 </sanitizer>
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
72 </param>
4
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
73 </when>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
74 </conditional>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
75 </inputs>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
76 <outputs>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
77 <data format="vcf" name="out_file1" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
78 </outputs>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
79 <tests>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
80 <test>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
81 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
82 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
83 <param name="reference_source_selector" value="history" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
84 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
85 <param name="isect_union" value="-i" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
86 <param name="invert" value="False" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
87 <param name="loci" value="False" />
5
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
88 <param name="adv_options_selector" value="no" />
4
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
89 <param name="window_size" value="30" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
90 <output name="out_file1" file="vcfvcfintersect-test1.vcf"/>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
91 </test>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
92 <test>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
93 <param name="reference_source_selector" value="history" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
94 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
95 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
96 <param name="isect_union" value="-u" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
97 <param name="invert" value="False" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
98 <param name="loci" value="False" />
5
c2026da116b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
parents: 4
diff changeset
99 <param name="adv_options_selector" value="no" />
4
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
100 <param name="window_size" value="30" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
101 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
102 <output name="out_file1" file="vcfvcfintersect-test2.vcf"/>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
103 </test>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
104 </tests>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
105 <help>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
106 Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp.
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
107
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
108 The options are::
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
109
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
110 -v, --invert invert the selection, printing only records which would
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
111 -i, --intersect-vcf FILE use this VCF for set intersection generation
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
112 -u, --union-vcf FILE use this VCF for set union generation
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
113 -w, --window-size N compare records up to this many bp away (default 30)
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
114 -l, --loci output whole loci when one alternate allele matches
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
115 -m, --ref-match intersect on the basis of record REF string
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
116 -t, --tag TAG attach TAG to each record's info field if it would intersect
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
117 -V, --tag-value VAL use this value to indicate that the allele is passing
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
118 '.' will be used otherwise. default: 'PASS'
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
119 -M, --merge-from FROM-TAG
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
120 -T, --merge-to TO-TAG merge from FROM-TAG used in the -i file, setting TO-TAG
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
121 in the current file.
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
122
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
123 ----
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
124
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
125 VCFVCFintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
126 </help>
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
127 <expand macro="citations" />
64d95a7df265 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 0
diff changeset
128 </tool>