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comparison macros.xml @ 0:a531317a3527 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
author iuc
date Mon, 02 May 2016 17:27:10 -0400
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children 8959eda17fca
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-1:000000000000 0:a531317a3527
1 <?xml version='1.0' encoding='utf-8'?>
2 <macros>
3 <token name="@VERSION@">1.2</token>
4 <xml name="requirements">
5 <requirements>
6 <!-- This requirement handles also bcftools from BioConda channel => https://github.com/bioconda/bioconda-recipes/tree/60d2ea750430dbe0191f6f8d5639f90fc1223bd9/recipes/bcftools/1.2 -->
7 <requirement type="package" version="1.2">bcftools</requirement>
8 </requirements>
9 </xml>
10 <xml name="version_command">
11 <version_command><![CDATA[bcftools 2>&1 | grep 'Version:']]></version_command>
12 </xml>
13 <xml name="citations">
14 <citations>
15 <citation type="doi">10.1093/bioinformatics/btp352</citation>
16 <yield />
17 </citations>
18 </xml>
19 <xml name="macro_exclude">
20 <param name="exclude" label="Exclude" help="exclude sites for which the expression is true (see man page for details)" />
21 </xml>
22 <xml name="macro_collapse">
23 <param name="collapse" label="Collapse" type="select" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
24 <option value="snps">snps</option>
25 <option value="indels">indels</option>
26 <option value="both">both</option>
27 <option value="all">all</option>
28 <option value="some">some</option>
29 <option value="none" selected="True">None</option>
30 </param>
31 </xml>
32 <xml name="macro_apply_filters_repeat">
33 <repeat name="apply_filters_repeat" title="Apply Filters">
34 <param name="apply_filters" label="Apply Filters" help="require at least one of the listed FILTER strings (e.g. &quot;PASS,.&quot;)" />
35 </repeat>
36 </xml>
37
38 <token name="@SEC_DEF_REGIONS@">
39 #if $sec_default.regions_file:
40 --regions-file "${sec_default.regions_file}"
41 #end if
42 </token>
43 <token name="@SEC_DEF_TARGETS@">
44 #if $sec_default.targets_file:
45 --targets-file "${sec_default.targets_file}"
46 #end if
47 </token>
48 <token name="@SEC_DEF_SAMPLES@">
49 #if $sec_default.samples_file:
50 --samples-file "${sec_default.samples_file}"
51 #end if
52 </token>
53
54 <xml name="macro_samples">
55 <param name="samples_file" label="Samples File" type="data" format="data" optional="True" help="file of samples to include" />
56 <param name="invert_samples_file" label="Invert Samples" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by the sample file selection" />
57 </xml>
58 <xml name="macro_targets">
59 <param name="targets_file" label="Targets File" type="data" format="data" optional="True" help="similar to -R but streams rather than index-jumps" />
60 <param name="invert_targets_file" label="Invert Targets" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by the target file selection" />
61 </xml>
62 <xml name="macro_regions">
63 <param name="regions_file" label="Regions File" type="data" format="data" optional="True" help="restrict to regions listed in a file" />
64 <param name="invert_regions_file" label="Invert Regions" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by region file selection" />
65 </xml>
66 <xml name="macro_select_output_type">
67 <param name="select_output_type" type="select">
68 <option value="v" selected="True">uncompressed VCF</option>
69 <option value="z">compressed VCF</option>
70 <option value="u">uncompressed BCF</option>
71 <option value="b">compressed BCF</option>
72 </param>
73 </xml>
74 </macros>