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comparison macros.xml @ 0:dabc1e7ca486 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
author iuc
date Thu, 19 Nov 2015 14:54:54 -0500
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children 3b0006e824c6
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-1:000000000000 0:dabc1e7ca486
1 <?xml version='1.0' encoding='utf-8'?>
2 <macros>
3 <token name="@VERSION@">1.2</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="1.2">bcftools</requirement>
7 </requirements>
8 </xml>
9 <xml name="version_command">
10 <version_command><![CDATA[bcftools 2>&1 | grep 'Version:']]></version_command>
11 </xml>
12 <xml name="citations">
13 <citations>
14 <citation type="doi">10.1093/bioinformatics/btp352</citation>
15 <yield />
16 </citations>
17 </xml>
18 <xml name="macro_exclude">
19 <param name="exclude" label="Exclude" help="exclude sites for which the expression is true (see man page for details)" />
20 </xml>
21 <xml name="macro_collapse">
22 <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">
23 <option value="snps">snps</option>
24 <option value="indels">indels</option>
25 <option value="both">both</option>
26 <option value="all">all</option>
27 <option value="some">some</option>
28 <option value="none" selected="True">None</option>
29 </param>
30 </xml>
31 <xml name="macro_apply_filters_repeat">
32 <repeat name="apply_filters_repeat" title="Apply Filters">
33 <param name="apply_filters" label="Apply Filters" help="require at least one of the listed FILTER strings (e.g. &quot;PASS,.&quot;)" />
34 </repeat>
35 </xml>
36
37 <token name="@SEC_DEF_REGIONS@">
38 #if $sec_default.regions_file:
39 --regions-file "${sec_default.regions_file}"
40 #end if
41 </token>
42 <token name="@SEC_DEF_TARGETS@">
43 #if $sec_default.targets_file:
44 --targets-file "${sec_default.targets_file}"
45 #end if
46 </token>
47 <token name="@SEC_DEF_SAMPLES@">
48 #if $sec_default.samples_file:
49 --samples-file "${sec_default.samples_file}"
50 #end if
51 </token>
52
53 <xml name="macro_samples">
54 <param name="samples_file" label="Samples File" type="data" format="data" optional="True" help="file of samples to include" />
55 <param name="invert_samples_file" label="Invert Samples" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by the sample file selection" />
56 </xml>
57 <xml name="macro_targets">
58 <param name="targets_file" label="Targets File" type="data" format="data" optional="True" help="similar to -R but streams rather than index-jumps" />
59 <param name="invert_targets_file" label="Invert Targets" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by the target file selection" />
60 </xml>
61 <xml name="macro_regions">
62 <param name="regions_file" label="Regions File" type="data" format="data" optional="True" help="restrict to regions listed in a file" />
63 <param name="invert_regions_file" label="Invert Regions" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by region file selection" />
64 </xml>
65 <xml name="macro_select_output_type">
66 <param name="select_output_type" type="select">
67 <option value="v" selected="True">uncompressed VCF</option>
68 <option value="z">compressed VCF</option>
69 <option value="u">uncompressed BCF</option>
70 <option value="b">compressed BCF</option>
71 </param>
72 </xml>
73 </macros>