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comparison mafFetch.xml @ 0:28fc170eb7cc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
author iuc
date Tue, 09 Sep 2025 16:20:41 +0000
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1 <tool id="ucsc_maffetch" name="mafFetch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description>Get overlapping records from an MAF using an index table</description>
3 <macros>
4 <token name="@TOOL_VERSION@">482</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 <token name="@PROFILE@">24.2</token>
7 </macros>
8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">ucsc-maffetch</requirement>
10 </requirements>
11 <command detect_errors="exit_code">
12 <![CDATA[
13 cp '$ucsc_db_connection' "\${HOME}/.hg.conf" &&
14 chmod 600 "\${HOME}/.hg.conf" &&
15 mafFetch '$genome' '$track' '$bed_file' out.maf
16 ]]>
17 </command>
18 <configfiles>
19 <configfile name="ucsc_db_connection"><![CDATA[
20 #European MariaDB server
21 db.host=genome-euro-mysql.soe.ucsc.edu
22 db.user=genomep
23 db.password=password
24 central.db=hgcentral
25 central.host=genome-euro-mysql.soe.ucsc.edu
26 central.user=genomep
27 central.password=password
28 gbdbLoc1=http://hgdownload.soe.ucsc.edu/gbdb/
29 forceTwoBit=on
30 ]]></configfile>
31 </configfiles>
32 <inputs>
33 <param name="bed_file" type="data" format="bed" label="Input BED file" help="Input BED file can be either BED6 or BED12"/>
34 <param name="genome" type="text" optional="false" label="Enter Genome database name" help="Name should match with the UCSC Table Browser Entries (For Eg. mm10, hg19, hg38)"/>
35 <param name="track" type="text" optional="false" label="Enter UCSC Table name for desired table of the above genome" help="Table name should match with the UCSC Table Browser Entries (For eg. knownGene, all_mrna)"/>
36 </inputs>
37 <outputs>
38 <data name="output" format="maf" from_work_dir="out.maf" label="${tool.name} on ${on_string}:Output MAF"/>
39 </outputs>
40 <tests>
41 <!-- Test 01: Testing with default options -->
42 <test expect_num_outputs="1">
43 <param name="bed_file" value="mafFetch.bed"/>
44 <param name="genome" value="hg19"/>
45 <param name="track" value="multiz46way"/>
46 <output name="output" ftype="maf">
47 <assert_contents>
48 <has_n_lines n="167"/>
49 <has_size value="17364"/>
50 </assert_contents>
51 </output>
52 </test>
53 </tests>
54 <help><![CDATA[
55
56 mafFetch is a command-line tool from the UCSC Genome Browser suite that extracts MAF records overlapping regions in a BED file (minimum 3 columns: chrom, start, end) from a specified UCSC database table (e.g., multiz46way for hg19). Outputs alignments to a MAF file using an indexed lookup for efficiency.
57
58 ]]></help>
59 <citations>
60 <citation type="bibtex">
61 @misc{mafFetch,
62 author = {Kent UCSC},
63 title = {mafFetch: A tool for get overlapping records from an MAF using an index table},
64 note = {Tool for get overlapping records from an MAF using an index table}
65 </citation>
66 </citations>
67 <creator>
68 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12" identifier="https://orcid.org/0009-0003-9935-828X"/>
69 <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
70 </creator>
71 </tool>