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comparison hal_halMaskExtract.xml @ 0:31871c901fe2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac
author iuc
date Fri, 06 Feb 2026 10:33:04 +0000
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-1:000000000000 0:31871c901fe2
1 <tool id="hal_halmaskextract" name="halMaskExtract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>extracts masked intervals of a genome into BED file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <command detect_errors="aggressive"><![CDATA[
9 halMaskExtract
10 #if $mode.regions == '--extend':
11 --extend $mode.extend
12 #else if $mode.regions == '--extendPct':
13 --extendPct $mode.extendPct
14 #end if
15 '$input_hal' '$refGenome' > '$out_file'
16 ]]></command>
17 <inputs>
18 <expand macro="input_hal"/>
19 <expand macro="params_refGenome"/>
20 <conditional name="mode">
21 <param name="regions" type="select" label="Extend masked regions">
22 <option value="" selected="true">No, don't extend</option>
23 <option value="--extend">Yes, extend by given number of bases (--extend)</option>
24 <option value="--extendPct">Yes, extend by percentage of their lengths (--extendPct)</option>
25 </param>
26 <when value=""/>
27 <when value="--extend">
28 <param name="extend" type="integer" min="0" value="0" label="Number of bases" help="Extend masked regions by given number of bases"/>
29 </when>
30 <when value="--extendPct">
31 <param name="extendPct" type="float" min="0" value="0" label="Percentage" help="Extend masked regions by percentage of their lengths"/>
32 </when>
33 </conditional>
34 </inputs>
35 <outputs>
36 <data name="out_file" format="bed" label="${tool.name} on ${on_string}"/>
37 </outputs>
38 <tests>
39 <test expect_num_outputs="1">
40 <param name="input_hal" value="halTestIndels.hal"/>
41 <param name="refGenome" value="Ref"/>
42 <output name="out_file" ftype="bed">
43 <assert_contents>
44 <has_line line="chr1&#009;5&#009;10"/>
45 <has_n_lines n="1"/>
46 </assert_contents>
47 </output>
48 </test>
49 <test expect_num_outputs="1">
50 <param name="input_hal" value="halTestIndels.hal"/>
51 <param name="refGenome" value="Ref"/>
52 <conditional name="mode">
53 <param name="regions" value="--extend"/>
54 <param name="extend" value="100"/>
55 </conditional>
56 <output name="out_file" ftype="bed">
57 <assert_contents>
58 <has_line line="chr1&#009;5&#009;100"/>
59 <has_n_lines n="1"/>
60 </assert_contents>
61 </output>
62 </test>
63 <test expect_num_outputs="1">
64 <param name="input_hal" value="halTestIndels.hal"/>
65 <param name="refGenome" value="Ref"/>
66 <conditional name="mode">
67 <param name="regions" value="--extendPct"/>
68 <param name="extendPct" value="0.25"/>
69 </conditional>
70 <output name="out_file" ftype="bed">
71 <assert_contents>
72 <has_line line="chr1&#009;4&#009;11"/>
73 <has_n_lines n="1"/>
74 </assert_contents>
75 </output>
76 </test>
77 </tests>
78 <help><![CDATA[
79 halMaskExtract extracts masked regions from a given genome found in an input HAL file and writes them as BED intervals.
80 Options let you extend intervals by a fixed number of bases or by a percentage of interval length.
81 ]]></help>
82 <expand macro="citation"/>
83 <expand macro="creator"/>
84 </tool>