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comparison hal_halSummarizeMutations.xml @ 0:daef75c08ab4 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 10:34:07 +0000
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-1:000000000000 0:daef75c08ab4
1 <tool id="hal_halsummarizemutations" name="halSummarizeMutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>creates a summary table of mutation events in the alignmet</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 halSummarizeMutations’s on failure.
10 halSummarizeMutations
11 #if $mode.option == '--rootGenome':
12 --rootGenome '$mode.rootGenome'
13 #else if $mode.option == '--targetGenomes':
14 --targetGenomes '$mode.targetGenomes'
15 #end if
16 --maxGap $maxGap
17 --maxNFraction $maxNFraction
18 $justSubs
19 ## Pipes output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
20 '$input_hal' | tr ',' '\t' > '$output_file'
21 ]]></command>
22 <inputs>
23 <expand macro="input_hal"/>
24 <conditional name="mode">
25 <param name="option" type="select" label="Summarize options">
26 <option value="" selected="true">All genomes (default)</option>
27 <option value="--targetGenomes">Specific target genomes (--targetGenomes)</option>
28 <option value="--rootGenome">Only genomes in a root genome subtree (--rootGenome)</option>
29 </param>
30 <when value=""/>
31 <when value="--rootGenome">
32 <expand macro="params_rootGenome"/>
33 </when>
34 <when value="--targetGenomes">
35 <expand macro="params_targetGenomes"/>
36 </when>
37 </conditional>
38 <expand macro="params_maxGap"/>
39 <expand macro="params_maxNFraction"/>
40 <param argument="--justSubs" type="boolean" truevalue="--justSubs" falsevalue="" checked="false" label="Just count substitutions" help="Results are total substitutions between genome and all children, rather than branch results. For tuning and performance checking only"/>
41 </inputs>
42 <outputs>
43 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Mutation events"/>
44 </outputs>
45 <tests>
46 <test expect_num_outputs="1">
47 <param name="input_hal" value="halTest.hal"/>
48 <output name="output_file" ftype="tabular">
49 <assert_contents>
50 <has_text text="GenomeName&#009; ParentName&#009; BranchLength"/>
51 <has_line line="Total&#009; &#009;3&#009; 15881&#009; 5274&#009; 0&#009; 0&#009; 0&#009; 12929&#009; 0&#009; 0&#009; 0&#009; 0&#009; 6&#009; 1304&#009; 0&#009; 0&#009; 0&#009; 0&#009; 28&#009; 8827&#009; 3&#009; 879&#009; 0"/>
52 <has_n_lines n="8"/>
53 </assert_contents>
54 </output>
55 </test>
56 <test expect_num_outputs="1">
57 <param name="input_hal" value="halTest.hal"/>
58 <conditional name="mode">
59 <param name="option" value="--rootGenome"/>
60 <param name="rootGenome" value="Genome_1"/>
61 </conditional>
62 <param name="justSubs" value="true"/>
63 <output name="output_file" ftype="tabular">
64 <assert_contents>
65 <has_text text="GenomeName&#009; ParentName&#009; BranchLength"/>
66 <has_line line="Total&#009; &#009;3&#009; 17639&#009; 5274&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0&#009; 0"/>
67 <has_n_lines n="9"/>
68 </assert_contents>
69 </output>
70 </test>
71 </tests>
72 <help><![CDATA[
73 halSummarizeMutations needs a HAL file as input and outputs a table that reports substitutions, indels, and other rearrangements across the alignment.
74 Focus the summary on selected genomes, a specific root genome, or the entire file.
75 The tool offers controls for how gaps and N rich regions are treated, and it can switch to a substitutions only mode for tuning and performance checking only.
76 ]]></help>
77 <expand macro="citation"/>
78 <expand macro="creator"/>
79 </tool>