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comparison hal_hal2paf.xml @ 0:9951a0cc9a11 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 10:38:12 +0000
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-1:000000000000 0:9951a0cc9a11
1 <tool id="hal_hal2paf" name="hal2paf" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>exports pairwise alignment to PAF</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 hal2paf
10 #if $rootGenome:
11 --rootGenome '$rootGenome'
12 #end if
13 $onlySequenceNames
14 '$input_hal' > temp.paf
15 #if $compression.type == 'gz':
16 && gzip -c temp.paf > '$out_file'
17 #else:
18 && mv temp.paf '$out_file'
19 #end if
20 ]]></command>
21 <inputs>
22 <expand macro="input_hal"/>
23 <expand macro="params_rootGenome_optional"/>
24 <expand macro="params_onlySequenceNames"/>
25 <conditional name="compression">
26 <param name="type" type="select" label="Compress output file">
27 <option value="" selected="true">Don't compress output file (default)</option>
28 <option value="gz">Compress output file to .gz</option>
29 </param>
30 <when value=""/>
31 <when value="gz"/>
32 </conditional>
33 </inputs>
34 <outputs>
35 <data name="out_file" format="paf" label="${tool.name} on ${on_string}: PAF">
36 <change_format>
37 <when input="compression.type" value="gz" format="paf.gz"/>
38 </change_format>
39 </data>
40 </outputs>
41 <tests>
42 <test expect_num_outputs="1">
43 <param name="input_hal" value="halTest.hal"/>
44 <output name="out_file" ftype="paf">
45 <assert_contents>
46 <has_line line="Genome_1.Genome_1_seq&#009;5472&#009;0&#009;1465&#009;+&#009;Genome_0.Genome_0_seq&#009;1758&#009;0&#009;1465&#009;1465&#009;1465&#009;255&#009;cg:Z:1465M"/>
47 <has_line line="Genome_2.Genome_2_seq&#009;4270&#009;2051&#009;2344&#009;+&#009;Genome_0.Genome_0_seq&#009;1758&#009;293&#009;586&#009;293&#009;293&#009;255&#009;cg:Z:293M"/>
48 <has_line line="Genome_3.Genome_3_seq&#009;6139&#009;3809&#009;4688&#009;+&#009;Genome_0.Genome_0_seq&#009;1758&#009;586&#009;1465&#009;879&#009;879&#009;255&#009;cg:Z:879M"/>
49 <has_n_lines n="25"/>
50 </assert_contents>
51 </output>
52 </test>
53 <test expect_num_outputs="1">
54 <param name="input_hal" value="halTest.hal"/>
55 <conditional name="compression">
56 <param name="type" value="gz"/>
57 </conditional>
58 <output name="out_file" ftype="paf.gz" file="hal2paf_output.paf.gz"/>
59 </test>
60 <test expect_num_outputs="1">
61 <param name="input_hal" value="halTest.hal"/>
62 <param name="rootGenome" value="Genome_0"/>
63 <param name="onlySequenceNames" value="true"/>
64 <output name="out_file" ftype="paf">
65 <assert_contents>
66 <has_line line="Genome_1_seq&#009;5472&#009;0&#009;1465&#009;+&#009;Genome_0_seq&#009;1758&#009;0&#009;1465&#009;1465&#009;1465&#009;255&#009;cg:Z:1465M"/>
67 <has_line line="Genome_2_seq&#009;4270&#009;2051&#009;2344&#009;+&#009;Genome_0_seq&#009;1758&#009;293&#009;586&#009;293&#009;293&#009;255&#009;cg:Z:293M"/>
68 <has_line line="Genome_3_seq&#009;6139&#009;3809&#009;4688&#009;+&#009;Genome_0_seq&#009;1758&#009;586&#009;1465&#009;879&#009;879&#009;255&#009;cg:Z:879M"/>
69 <has_n_lines n="25"/>
70 </assert_contents>
71 </output>
72 </test>
73 </tests>
74 <help><![CDATA[
75 hal2paf exports each branch of an input HAL file as a pairwise alignment in PAF format.
76 ]]></help>
77 <expand macro="citation"/>
78 <expand macro="creator"/>
79 </tool>