Mercurial > repos > iuc > bcftools_isec

comparison bcftools_isec.xml @ 0:a994b57c9a7d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:03:54 -0400
parents
children 71747e4a4aa1
comparison
equal deleted inserted replaced
-1:000000000000 0:a994b57c9a7d
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
3 <description>Create intersections, unions and complements of VCF files</description>
4 <macros>
5 <token name="@EXECUTABLE@">isec</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="version_command" />
10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@
12 @PREPARE_INPUT_FILES@
13 #set $section = $sec_restrict
14 @PREPARE_TARGETS_FILE@
15
16 bcftools @EXECUTABLE@
17
18 ## Default section
19 #set $section = $sec_default
20 ${section.complement}
21 #if $section.nfiles:
22 --nfiles "${section.nfiles}"
23 #end if
24
25 #set $section = $sec_restrict
26 @REGIONS@
27 @TARGETS@
28 @COLLAPSE@
29 @APPLY_FILTERS@
30 @INCLUDE@
31 @EXCLUDE@
32
33 @OUTPUT_TYPE@
34 @THREADS@
35
36 ## Primary Input/Outputs
37 @INPUT_FILES@
38 > "$output_file"
39
40 ]]>
41 </command>
42 <inputs>
43 <expand macro="macro_inputs" />
44 <section name="sec_restrict" expanded="false" title="Restrict to">
45 <expand macro="macro_collapse" />
46 <expand macro="macro_include" />
47 <expand macro="macro_exclude" />
48 <expand macro="macro_apply_filters" />
49 <expand macro="macro_regions" />
50 <expand macro="macro_targets" />
51 </section>
52 <section name="sec_default" expanded="true" title="Isec Options">
53 <param name="nfiles" type="text" label="Nfiles" optional="True"
54 help="Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files" >
55 <validator type="regex" message="bitmask zero or one">^([=+-]?\d+|~[01]+)?$</validator>
56 </param>
57 <param name="complement" type="boolean" truevalue="--complement" falsevalue="" label="Complement"
58 help="Output positions present only in the first file but missing in the others" />
59 <param name="prefix" type="boolean" truevalue="--prefix subset" falsevalue="" checked="false" label="subset each of the input files"
60 help="(-p)" />
61 <param name="write" type="text" label="Files to write" optional="True"
62 help="(-write) The output files to write " >
63 <validator type="regex" message="">^([=+-]?\d+|~[01]+)?$</validator>
64 </param>
65 </section>
66 <expand macro="macro_select_output_type" />
67 </inputs>
68 <outputs>
69 <expand macro="macro_vcf_output"/>
70 </outputs>
71 <tests>
72 <test>
73 <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" />
74 <param name="nfiles" value="=2" />
75 <param name="output_type" value="v" />
76 <output name="output_file">
77 <assert_contents>
78 <has_text text="3157410" />
79 <has_text text="3162006" />
80 <not_has_text text="3062915" />
81 </assert_contents>
82 </output>
83 </test>
84
85 </tests>
86 <help><![CDATA[
87 =====================================
88 bcftools @EXECUTABLE@
89 =====================================
90
91 Create intersections, unions and complements of VCF files.
92
93 @COLLAPSE_HELP@
94 @REGIONS_HELP@
95 @TARGETS_HELP@
96 @EXPRESSIONS_HELP@
97
98 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
99
100 @BCFTOOLS_WIKI@
101 ]]>
102 </help>
103 <expand macro="citations" />
104 </tool>