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comparison hal_halBranchMutations.xml @ 0:a84e089a22f8 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 10:35:23 +0000
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-1:000000000000 0:a84e089a22f8
1 <tool id="hal_halbranchmutations" name="halBranchMutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>identifies mutations on a branch between given genome and its parent</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 halBranchMutations
10 #if $support.file == 'true':
11 --refTargets '$support.refTargets'
12 #end if
13 #if $mode.export == 'sequence':
14 --refSequence '$mode.sequence'
15 #end if
16 --start $start
17 --length $length
18 --maxGap $maxGap
19 --maxNFraction $maxNFraction
20 --refFile stdout
21 --snpFile stdout
22 --delBreakFile stdout
23 --parentFile '$output_parentFile'
24 '$input_hal' '$refGenome' > '$output_file'
25 ]]></command>
26 <inputs>
27 <expand macro="input_hal"/>
28 <param name="refGenome" type="text" value="" label="Reference genome" help="To be analyzed branch and its according parent. Must denote bottom node in a branch, and therefore cannot be the root itself">
29 <expand macro="sanitizer_default"/>
30 <expand macro="validator_trim"/>
31 </param>
32 <conditional name="support">
33 <param name="file" type="select" label="Use a BED file for coordinates" help="Use a BED file to define intervals in the reference genome to process">
34 <option value="false" selected="true">No, don't use a BED file (default)</option>
35 <option value="true">Yes, use a BED file (--refTargets)</option>
36 </param>
37 <when value="false"/>
38 <when value="true">
39 <param name="refTargets" type="data" format="bed" label="BED file"/>
40 </when>
41 </conditional>
42 <conditional name="mode">
43 <param name="export" type="select" label="Sequence process options">
44 <option value="default" selected="true">Process all sequences (default)</option>
45 <option value="sequence">Process a reference sequence (--refSequence)</option>
46 </param>
47 <when value="default"/>
48 <when value="sequence">
49 <expand macro="params_sequence"/>
50 </when>
51 </conditional>
52 <expand macro="params_start"/>
53 <expand macro="params_length"/>
54 <expand macro="params_maxGap"/>
55 <expand macro="params_maxNFraction"/>
56 </inputs>
57 <outputs>
58 <data name="output_file" format="bed" label="${tool.name} on ${on_string}"/>
59 <data name="output_parentFile" format="bed" label="${tool.name} on ${on_string}: Rearrangements in reference's parent genome"/>
60 </outputs>
61 <tests>
62 <test expect_num_outputs="2">
63 <param name="input_hal" value="halTest.hal"/>
64 <param name="refGenome" value="Genome_1"/>
65 <output name="output_file" ftype="bed">
66 <assert_contents>
67 <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
68 <has_line line="Genome_1_seq&#009;1465&#009;1758&#009;I&#009;Genome_0&#009;Genome_1"/>
69 <has_line line="Genome_1_seq&#009;4395&#009;4688&#009;P&#009;Genome_0&#009;Genome_1"/>
70 <has_n_lines n="5"/>
71 </assert_contents>
72 </output>
73 <output name="output_parentFile" ftype="bed">
74 <assert_contents>
75 <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
76 <has_line line="Genome_0_seq&#009;293&#009;879&#009;U&#009;Genome_0&#009;Genome_1"/>
77 <has_line line="Genome_0_seq&#009;586&#009;879&#009;U&#009;Genome_0&#009;Genome_1"/>
78 <has_n_lines n="13"/>
79 </assert_contents>
80 </output>
81 </test>
82 <test expect_num_outputs="2">
83 <param name="input_hal" value="halTest.hal"/>
84 <param name="refGenome" value="Genome_1"/>
85 <param name="start" value="10"/>
86 <param name="length" value="500"/>
87 <output name="output_file" ftype="bed">
88 <assert_contents>
89 <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
90 <has_n_lines n="2"/>
91 </assert_contents>
92 </output>
93 <output name="output_parentFile" ftype="bed">
94 <assert_contents>
95 <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
96 <has_line line="Genome_0_seq&#009;293&#009;879&#009;U&#009;Genome_0&#009;Genome_1"/>
97 <has_n_lines n="3"/>
98 </assert_contents>
99 </output>
100 </test>
101 <test expect_num_outputs="2">
102 <param name="input_hal" value="halTest.hal"/>
103 <param name="refGenome" value="Genome_1"/>
104 <conditional name="mode">
105 <param name="export" value="sequence"/>
106 <param name="sequence" value="Genome_1_seq"/>
107 </conditional>
108 <output name="output_file" ftype="bed">
109 <assert_contents>
110 <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
111 <has_line line="Genome_1_seq&#009;1465&#009;1758&#009;I&#009;Genome_0&#009;Genome_1"/>
112 <has_line line="Genome_1_seq&#009;4395&#009;4688&#009;P&#009;Genome_0&#009;Genome_1"/>
113 <has_n_lines n="5"/>
114 </assert_contents>
115 </output>
116 <output name="output_parentFile" ftype="bed">
117 <assert_contents>
118 <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
119 <has_line line="Genome_0_seq&#009;293&#009;879&#009;U&#009;Genome_0&#009;Genome_1"/>
120 <has_line line="Genome_0_seq&#009;586&#009;879&#009;U&#009;Genome_0&#009;Genome_1"/>
121 <has_n_lines n="13"/>
122 </assert_contents>
123 </output>
124 </test>
125 <test expect_num_outputs="2">
126 <param name="input_hal" value="halTest.hal"/>
127 <param name="refGenome" value="Genome_1"/>
128 <conditional name="support">
129 <param name="file" value="true"/>
130 <param name="refTargets" value="halBranchMutations.bed"/>
131 </conditional>
132 <output name="output_file" ftype="bed">
133 <assert_contents>
134 <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
135 <has_line line="Genome_1_seq&#009;1465&#009;1758&#009;I&#009;Genome_0&#009;Genome_1"/>
136 <has_line line="Genome_1_seq&#009;4395&#009;4688&#009;P&#009;Genome_0&#009;Genome_1"/>
137 <has_n_lines n="5"/>
138 </assert_contents>
139 </output>
140 <output name="output_parentFile" ftype="bed">
141 <assert_contents>
142 <has_line line="#Sequence&#009;Start&#009;End&#009;MutationID&#009;ParentGenome&#009;ChildGenome"/>
143 <has_line line="Genome_0_seq&#009;586&#009;879&#009;U&#009;Genome_0&#009;Genome_1"/>
144 <has_line line="Genome_0_seq&#009;1172&#009;1465&#009;U&#009;Genome_0&#009;Genome_1"/>
145 <has_n_lines n="13"/>
146 </assert_contents>
147 </output>
148 </test>
149 </tests>
150 <help><![CDATA[
151 halBranchMutations detects mutations that occurred on the branch between a chosen genome and its parent in a HAL alignment.
152 It reports point mutations, deletions, duplications, and other structural changes in an output BED file.
153 ]]></help>
154 <expand macro="citation"/>
155 <expand macro="creator"/>
156 </tool>