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comparison hal_halRenameSequences.xml @ 0:4dd28ce079d0 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 10:37:36 +0000
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-1:000000000000 0:4dd28ce079d0
1 <tool id="hal_halrenamesequences" name="halRenameSequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>renames sequences of a genome in a HAL 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 ## Copy input HAL to ensure that it is not modified.
10 cp '$input_hal' writable_hal.hal &&
11 halRenameSequences
12 writable_hal.hal '$refGenome' '$input_mapping'
13 ]]></command>
14 <inputs>
15 <expand macro="input_hal"/>
16 <expand macro="params_refGenome"/>
17 <expand macro="input_mapping"/>
18 </inputs>
19 <outputs>
20 <data name="out_file" format="hal" label="${tool.name} on ${on_string}" from_work_dir="writable_hal.hal"/>
21 </outputs>
22 <tests>
23 <test expect_num_outputs="1">
24 <param name="input_hal" value="halTest.hal"/>
25 <param name="refGenome" value="Genome_1"/>
26 <param name="input_mapping" value="halRenameSequences_input.txt"/>
27 <output name="out_file" ftype="hal">
28 <assert_contents>
29 <has_size min="50000"/>
30 </assert_contents>
31 </output>
32 <assert_stdout>
33 <has_line line="Renaming Genome_1_seq to Genome_test_1_seq"/>
34 </assert_stdout>
35 </test>
36 <test expect_num_outputs="1">
37 <param name="input_hal" value="halTest.hal"/>
38 <param name="refGenome" value="Genome_1"/>
39 <param name="input_mapping" value="halRenameSequences_input.tsv"/>
40 <output name="out_file" ftype="hal">
41 <assert_contents>
42 <has_size min="50000"/>
43 </assert_contents>
44 </output>
45 <assert_stdout>
46 <has_line line="Renaming Genome_1_seq to Genome_test_1_seq"/>
47 </assert_stdout>
48 </test>
49 </tests>
50 <help><![CDATA[
51 halRenameSequences renames sequence names for a given reference genome from an input HAL file.
52 Sequence names are updated according to an input tab-separated mapping file.
53 Each row specifies an old sequence name and its corresponding new name.
54 Only sequences listed in the mapping file are renamed.
55 All other sequence names in the given reference genome remain unchanged.
56
57 A new HAL file is created as output instead of modifying the input HAL file.
58 ]]></help>
59 <expand macro="citation"/>
60 <expand macro="creator"/>
61 </tool>