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comparison hal_halSnps.xml @ 0:116020f2c8f3 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 10:35:08 +0000
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-1:000000000000 0:116020f2c8f3
1 <tool id="hal_halsnps" name="halSnps" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>counts SNPs between orthologous positions in multiple genomes</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 set -o pipefail; ## Sets the pipeline’s exit code to halSnps on failure.
10 ( ## echo headers for specific numerical data
11 echo -e "targetGenome\ttotalSnps\ttotalCleanOrthologousPairs";
12 halSnps
13 #if $mode.export == 'sequence':
14 --refSequence '$mode.sequence'
15 #end if
16 --start $start
17 --length $length
18 --minSpeciesForSnp $minSpeciesForSnp
19 $noDupes
20 $unique
21 '$input_hal' '$refGenome' '$targetGenomes'
22 | tr ' ' '\t' ## Pipes specific output to replace space with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
23 ) > '$out_file'
24 ]]></command>
25 <inputs>
26 <expand macro="input_hal"/>
27 <expand macro="params_refGenome"/>
28 <expand macro="params_targetGenomes"/>
29 <conditional name="mode">
30 <param name="export" type="select" label="Process options">
31 <option value="default" selected="true">Process all sequences (default)</option>
32 <option value="sequence">Process a specific sequence (--refSequence)</option>
33 </param>
34 <when value="default"/>
35 <when value="sequence">
36 <expand macro="params_sequence"/>
37 </when>
38 </conditional>
39 <expand macro="params_start"/>
40 <expand macro="params_length"/>
41 <param argument="--noDupes" type="boolean" truevalue="--noDupes" falsevalue="" checked="false" label="No duplicates" help="Do not consider paralogies while mapping"/>
42 <param argument="--minSpeciesForSnp" type="integer" min="1" value="1" label="Minimum number of species" help="Minimum number of species that must have a different base than the reference for a SNP to be reported in the output"/>
43 <param argument="--unique" type="boolean" truevalue="--unique" falsevalue="" checked="false" label="Unique" help="Whether to ignore columns that are not canonical on the reference genome"/>
44 </inputs>
45 <outputs>
46 <data name="out_file" format="tabular" label="${tool.name} on ${on_string}"/>
47 </outputs>
48 <tests>
49 <test expect_num_outputs="1">
50 <param name="input_hal" value="halTest.hal"/>
51 <param name="refGenome" value="Genome_0"/>
52 <param name="targetGenomes" value="Genome_0,Genome_1,Genome_2"/>
53 <output name="out_file" ftype="tabular">
54 <assert_contents>
55 <has_line line="targetGenome&#009;totalSnps&#009;totalCleanOrthologousPairs"/>
56 <has_line line="Genome_0&#009;0&#009;1758"/>
57 <has_line line="Genome_2&#009;0&#009;586"/>
58 <has_n_lines n="4"/>
59 </assert_contents>
60 </output>
61 </test>
62 <test expect_num_outputs="1">
63 <param name="input_hal" value="halTest.hal"/>
64 <param name="refGenome" value="Genome_0"/>
65 <param name="targetGenomes" value="Genome_0,Genome_1,Genome_2"/>
66 <param name="noDupes" value="true"/>
67 <output name="out_file" ftype="tabular">
68 <assert_contents>
69 <has_line line="targetGenome&#009;totalSnps&#009;totalCleanOrthologousPairs"/>
70 <has_line line="Genome_0&#009;0&#009;0"/>
71 <has_line line="Genome_2&#009;0&#009;1465"/>
72 <has_n_lines n="4"/>
73 </assert_contents>
74 </output>
75 </test>
76 <test expect_num_outputs="1">
77 <param name="input_hal" value="halTest.hal"/>
78 <param name="refGenome" value="Genome_0"/>
79 <param name="targetGenomes" value="Genome_0,Genome_1,Genome_2"/>
80 <param name="start" value="10"/>
81 <param name="length" value="50"/>
82 <output name="out_file" ftype="tabular">
83 <assert_contents>
84 <has_line line="targetGenome&#009;totalSnps&#009;totalCleanOrthologousPairs"/>
85 <has_line line="Genome_0&#009;0&#009;50"/>
86 <has_line line="Genome_2&#009;0&#009;50"/>
87 <has_n_lines n="4"/>
88 </assert_contents>
89 </output>
90 </test>
91 <test expect_num_outputs="1">
92 <param name="input_hal" value="halTest.hal"/>
93 <param name="refGenome" value="Genome_0"/>
94 <param name="targetGenomes" value="Genome_0,Genome_1,Genome_2"/>
95 <conditional name="mode">
96 <param name="export" value="sequence"/>
97 <param name="sequence" value="Genome_0_seq"/>
98 </conditional>
99 <param name="start" value="10"/>
100 <param name="length" value="500"/>
101 <output name="out_file" ftype="tabular">
102 <assert_contents>
103 <has_line line="targetGenome&#009;totalSnps&#009;totalCleanOrthologousPairs"/>
104 <has_line line="Genome_0&#009;0&#009;500"/>
105 <has_line line="Genome_2&#009;0&#009;283"/>
106 <has_n_lines n="4"/>
107 </assert_contents>
108 </output>
109 </test>
110 </tests>
111 <help><![CDATA[
112 halSnps counts SNPs between orthologous positions across multiple genomes in a HAL alignment.
113 The tool compares each position in a reference genome against one or more target genomes and reports how many SNPs occur, along with the number of clean orthologous positions examined.
114 ]]></help>
115 <expand macro="citation"/>
116 <expand macro="creator"/>
117 </tool>