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comparison mafFrag.xml @ 0:e452e9e359e7 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 16:20:32 +0000
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1 <tool id="ucsc_maffrag" name="mafFrag" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description>Extract MAF sequences for a region from database</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-maffrag</requirement>
10 </requirements>
11 <command detect_errors="exit_code">
12 <![CDATA[
13 cp '$ucsc_db_connection' "\${HOME}/.hg.conf" &&
14 chmod 600 "\${HOME}/.hg.conf" &&
15 mafFrag '$genome' '$track' '$chrom' '$start' '$end' '$strand' out.maf
16 ]]>
17 </command>
18 <configfiles>
19 <configfile name="ucsc_db_connection"><![CDATA[
20 #European MariaDB server
21 db.host=genome-euro-mysql.soe.ucsc.edu
22 db.user=genomep
23 db.password=password
24 central.db=hgcentral
25 central.host=genome-euro-mysql.soe.ucsc.edu
26 central.user=genomep
27 central.password=password
28 gbdbLoc1=http://hgdownload.soe.ucsc.edu/gbdb/
29 forceTwoBit=on
30 ]]></configfile>
31 </configfiles>
32 <inputs>
33 <param name="genome" type="text" optional="false" label="Enter Genome database name" help="Name should match with the UCSC Table Browser Entries (For Eg. mm10, hg19, hg38)"/>
34 <param name="track" type="text" optional="false" label="Enter UCSC Table name for desired table of the above genome" help="Table name should match with the UCSC Table Browser Entries (For eg. knownGene, all_mrna)"/>
35 <param name="chrom" type="text" optional="false" label="Chromosome" help="Chromosome name (e.g., chr1, chr2, etc.)"/>
36 <param name="start" type="integer" optional="false" label="Start position" help="Start position of the region in the chromosome (0-based)"/>
37 <param name="end" type="integer" optional="false" label="End position" help="End position of the region in the chromosome (0-based)"/>
38 <param name="strand" type="select" optional="false" label="Strand" help="Strand of the region">
39 <option value=".">No Strand</option>
40 <option value="+">Forward Strand(+)</option>
41 <option value="-">Reverse Strand(-)</option>
42 </param>
43 </inputs>
44 <outputs>
45 <data name="output" format="maf" from_work_dir="out.maf" label="${tool.name} on ${on_string}:Output MAF"/>
46 </outputs>
47 <tests>
48 <!-- Test 01: Testing with default options -->
49 <test expect_num_outputs="1">
50 <param name="genome" value="hg19"/>
51 <param name="track" value="multiz46way"/>
52 <param name="chrom" value="chr17"/>
53 <param name="start" value="7578370"/>
54 <param name="end" value="7578400"/>
55 <param name="strand" value="+"/>
56 <output name="output" ftype="maf">
57 <assert_contents>
58 <has_n_lines n="43"/>
59 <has_size value="3087"/>
60 <has_line line="s hg19.chr17 7578370 30 + 81195210 CA---TCGCTA----TCTGAG--CAGCGCTC-ATGGTGGG"/>
61 </assert_contents>
62 </output>
63 </test>
64 </tests>
65 <help><![CDATA[
66
67 mafFrag is a command-line tool from the UCSC Genome Browser suite that extracts MAF sequences for a region from database.
68
69 ]]></help>
70 <citations>
71 <citation type="bibtex">
72 @misc{mafFrag,
73 author = {Kent UCSC},
74 title = {mafFrag: A tool that extracts MAF sequences for a region from database},
75 note = {Tool that extracts MAF sequences for a region from database}
76 </citation>
77 </citations>
78 <creator>
79 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12" identifier="https://orcid.org/0009-0003-9935-828X"/>
80 <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
81 </creator>
82 </tool>