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comparison vcfvcfintersect.xml @ 2:c7314b925161 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect commit 93df3895fbf2fa44ff279303093fb89b79081687
author devteam
date Thu, 15 Sep 2016 13:30:27 -0400
parents b29dbe1270b5
children 6f6bf10618d7
comparison
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1:d3f4f86a18d4 2:c7314b925161
1 <tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="0.0.3"> 1 <tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="@WRAPPER_VERSION@.0">
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"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio"></expand> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 #set $reference_fasta_filename = "localref.fa"
10 #if str( $reference_source.reference_source_selector ) == "history":
11 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
12 #else:
13 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
14 #end if
9 15
10 #set $reference_fasta_filename = "localref.fa" 16 #if $adv_options.adv_options_selector == "use_adv_controls":
11 #if str( $reference_source.reference_source_selector ) == "history": 17 vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}"
12 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 18 #else:
13 #else: 19 vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}"
14 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 20 #end if
15 #end if 21 </command>
16 22 <inputs>
17 #if $adv_options.adv_options_selector == True: 23 <!-- selecting refernce source -->
18 24 <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" />
19 vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" 25 <param name="vcf_input2" type="data" format="vcf" label="The second VCF dataset"
20 26 help="The second dataset will be instersected with the first"/>
21 #else: 27 <conditional name="reference_source">
22 28 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"
23 vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" 29 help="This tools needs to access reference genomes sequence specified by this option.">
24 30 <option value="cached">Locally cached</option>
25 #end if 31 <option value="history">History</option>
26 32 </param>
27 </command> 33 <when value="cached">
28 <inputs> 34 <param name="ref_file" type="select" label="Select reference genome">
29 <!-- selecting refernce source --> 35 <options from_data_table="fasta_indexes">
30 <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" /> 36 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
31 <param name="vcf_input2" type="data" format="vcf" label="The second VCF dataset" help="The second dataset will be instersected with the first"/> 37 </options>
32 <conditional name="reference_source"> 38 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
33 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome" help="This tools needs to access reference genomes sequence specified by this option."> 39 </param>
34 <option value="cached">Locally cached</option> 40 </when>
35 <option value="history">History</option> 41 <when value="history"> <!-- FIX ME!!!! -->
36 </param> 42 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
37 <when value="cached"> 43 </when>
38 <param name="ref_file" type="select" label="Select reference genome"> 44 </conditional>
39 <options from_data_table="fasta_indexes"> 45 <param name="isect_union" type="select" label="Union or intersection" help="-i or -u">
40 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> 46 <option value="-i">Intersect</option>
41 </options> 47 <option value="-u">Union</option>
42 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 48 </param>
43 </param> 49 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert" />
44 </when> 50 <param name="window_size" type="integer" value="30"
45 <when value="history"> <!-- FIX ME!!!! --> 51 label="compare records up to this many bp away (window size)" help="-w, --window-size" />
46 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> 52 <param name="loci" type="boolean" truevalue="-l" falsevalue=""
47 </when> 53 label="output whole loci when one alternate allele matches" help="-l, --loci" />
48 </conditional> 54 <conditional name="adv_options">
49 <param name="isect_union" type="select" label="Union or intersection" help="-i or -u"> 55 <param name="adv_options_selector" type="select" label="Advanced controls" help="Allows you to specify options that are not listed above">
50 <option value="-i">Intersect</option> 56 <option value="no">Don't use advanced options</option>
51 <option value="-u">Union</option> 57 <option value="use_adv_controls">Use advanced options</option>
52 </param> 58 </param>
53 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert" /> 59 <when value="no" />
54 <param name="window_size" type="integer" value="30" label="compare records up to this many bp away (window size)" help="-w, --window-size" /> 60 <when value="use_adv_controls">
55 <param name="loci" type="boolean" truevalue="-l" falsevalue="" label="output whole loci when one alternate allele matches" help="-l, --loci" /> 61 <param name="adv_options_input" type="text" value="-t &quot;vcfvcf-intersect-result&quot;"
56 <conditional name="adv_options"> 62 label="Enter additional command line options described in the help section below"
57 <param name="adv_options_selector" type="boolean" truevalue="use_adv_controls" label="Advanced controls" help="Allows you to specify options that are not listed above"/> 63 help="such as -m, -t, -V, -M, and -T" />
58 <when value="use_adv_controls"> 64 <sanitizer>
59 <param name="adv_options_input" type="text" value="-t &quot;vcfvcf-intersect-result&quot;" label="Enter additional command line options described in the help section below" help="such as -m, -t, -V, -M, and -T" /> 65 <valid initial="string.printable">
60 <sanitizer> 66 <remove value="&apos;"/>
61 <valid initial="string.printable"> 67 </valid>
62 <remove value="&apos;"/> 68 <mapping initial="none">
63 </valid> 69 <add source="&apos;" target="__sq__"/>
64 <mapping initial="none"> 70 </mapping>
65 <add source="&apos;" target="__sq__"/> 71 </sanitizer>
66 </mapping> 72 </when>
67 </sanitizer> 73 </conditional>
68 </when> 74 </inputs>
69 </conditional> 75 <outputs>
70 </inputs> 76 <data format="vcf" name="out_file1" />
71 <outputs> 77 </outputs>
72 <data format="vcf" name="out_file1" /> 78 <tests>
73 </outputs> 79 <test>
74 <tests> 80 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
75 <test> 81 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />
76 <param name="reference_source_selector" value="history" /> 82 <param name="reference_source_selector" value="history" />
77 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> 83 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
78 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> 84 <param name="isect_union" value="-i" />
79 <param name="isect_union" value="-i" /> 85 <param name="invert" value="False" />
80 <param name="invert" value="False" /> 86 <param name="loci" value="False" />
81 <param name="loci" value="False" /> 87 <patam name="adv_options_selector" value="no" />
82 <patam name="adv_options" value="False" /> 88 <param name="window_size" value="30" />
83 <param name="window_size" value="30" /> 89 <output name="out_file1" file="vcfvcfintersect-test1.vcf"/>
84 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> 90 </test>
85 <output name="out_file1" file="vcfvcfintersect-test1.vcf"/> 91 <test>
86 </test> 92 <param name="reference_source_selector" value="history" />
87 <test> 93 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
88 <param name="reference_source_selector" value="history" /> 94 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />
89 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> 95 <param name="isect_union" value="-u" />
90 <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> 96 <param name="invert" value="False" />
91 <param name="isect_union" value="-u" /> 97 <param name="loci" value="False" />
92 <param name="invert" value="False" /> 98 <patam name="adv_options_selector" value="no" />
93 <param name="loci" value="False" /> 99 <param name="window_size" value="30" />
94 <patam name="adv_options" value="False" /> 100 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
95 <param name="window_size" value="30" /> 101 <output name="out_file1" file="vcfvcfintersect-test2.vcf"/>
96 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> 102 </test>
97 <output name="out_file1" file="vcfvcfintersect-test2.vcf"/>
98 </test>
99 </tests> 103 </tests>
100 <help> 104 <help>
101 105 Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp.
102 Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp.
103 106
104 The options are:: 107 The options are::
105 108
106 -v, --invert invert the selection, printing only records which would 109 -v, --invert invert the selection, printing only records which would
107 -i, --intersect-vcf FILE use this VCF for set intersection generation 110 -i, --intersect-vcf FILE use this VCF for set intersection generation
117 in the current file. 120 in the current file.
118 121
119 ---- 122 ----
120 123
121 VCFVCFintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). 124 VCFVCFintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
122 </help> 125 </help>
123 <expand macro="citations" /> 126 <expand macro="citations" />
124 </tool> 127 </tool>