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comparison mafCoverage.xml @ 0:2b1884fdb849 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit fe43201294560762b7aab73785df2f1f7828cb9e
author iuc
date Thu, 14 Aug 2025 11:59:27 +0000
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-1:000000000000 0:2b1884fdb849
1 <tool id="ucsc_mafcoverage" name="mafCoverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description>Analyse coverage by MAF files</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-mafcoverage</requirement>
10 </requirements>
11 <command detect_errors="exit_code">
12 <![CDATA[
13 cp '$ucsc_db_connection' "\${HOME}/.hg.conf" &&
14 chmod 600 "\${HOME}/.hg.conf" &&
15 mafCoverage
16 '$genome'
17 '$maf_file'
18 #if $restrict_option.restrict_select == "yes":
19 -restrict='$restrict_option.restrict_bed'
20 #end if
21 #if $count != "":
22 -count=$count
23 #end if
24 > coverage.txt
25 ]]>
26 </command>
27 <configfiles>
28 <configfile name="ucsc_db_connection"><![CDATA[
29 #European MariaDB server
30 db.host=genome-euro-mysql.soe.ucsc.edu
31 db.user=genomep
32 db.password=password
33 central.db=hgcentral
34 central.host=genome-euro-mysql.soe.ucsc.edu
35 central.user=genomep
36 central.password=password
37 gbdbLoc1=http://hgdownload.soe.ucsc.edu/gbdb/
38 forceTwoBit=on
39 ]]></configfile>
40 </configfiles>
41 <inputs>
42 <param name="maf_file" type="data" format="maf" label="Input MAF file" help="Input MAF file for which coverage needs to be analysed. MAF file must be sorted by chromosome, tStart"/>
43 <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)"/>
44 <conditional name="restrict_option">
45 <param name="restrict_select" type="select" label="Restrict to a specific parts of input BED file" help="Restrict the MAF coverage to a specific part of the input BED file. If not selected, the entire BED file will be used.">
46 <option value="no">No</option>
47 <option value="yes">Yes</option>
48 </param>
49 <when value="yes">
50 <param name="restrict_bed" type="data" format="bed" label="Restrict BED file" help="Select a BED file to restrict the MAF coverage to specific regions."/>
51 </when>
52 <when value="no"/>
53 </conditional>
54 <param name="count" type="integer" value="" optional="true" label="Number of matching species to count coverage" help="Number of species to count coverage for. Default is 3"/>
55 </inputs>
56 <outputs>
57 <data name="output" format="txt" from_work_dir="coverage.txt" label="${tool.name} on ${on_string}:Output Coverage"/>
58 </outputs>
59 <tests>
60 <!-- Test 01: Testing with default options -->
61 <test expect_num_outputs="1">
62 <param name="maf_file" value="mafFetch.maf"/>
63 <param name="genome" value="hg19"/>
64 <conditional name="restrict_option">
65 <param name="restrict_select" value="no"/>
66 </conditional>
67 <output name="output" ftype="txt">
68 <assert_contents>
69 <has_n_lines n="16"/>
70 <has_text_matching expression="all\t330\t0.00\t170\t0.00\t25\t0.00\t145\t0.00"/>
71 <has_text_matching expression="chr13\t214\t0.00\t101\t0.00\t17\t0.00\t84\t0.00"/>
72 <has_text_matching expression="chr17\t116\t0.00\t69\t0.00\t8\t0.00\t61\t0.00"/>
73 </assert_contents>
74 </output>
75 </test>
76
77 <!-- Test 02: Testing -count option -->
78 <test expect_num_outputs="1">
79 <param name="maf_file" value="mafFetch.maf"/>
80 <param name="genome" value="hg19"/>
81 <conditional name="restrict_option">
82 <param name="restrict_select" value="no"/>
83 </conditional>
84 <param name="count" value="2"/>
85 <output name="output" ftype="txt">
86 <assert_contents>
87 <has_n_lines n="16"/>
88 <has_text_matching expression="all\t330\t0.00\t170\t0.00\t25\t0.00\t145\t0.00"/>
89 <has_text_matching expression="chr13\t214\t0.00\t101\t0.00\t17\t0.00\t84\t0.00"/>
90 <has_text_matching expression="chr17\t116\t0.00\t69\t0.00\t8\t0.00\t61\t0.00"/>
91 </assert_contents>
92 </output>
93 </test>
94
95 <!-- Test 03: Testing with restrict option -->
96 <test expect_num_outputs="1">
97 <param name="maf_file" value="mafFetch.maf"/>
98 <param name="genome" value="hg19"/>
99 <conditional name="restrict_option">
100 <param name="restrict_select" value="yes"/>
101 <param name="restrict_bed" value="restrict.bed"/>
102 </conditional>
103 <param name="count" value="3"/>
104 <output name="output" ftype="txt">
105 <assert_contents>
106 <has_n_lines n="17"/>
107 <has_text_matching expression="all\t207\t94.09\t78\t35.45\t6\t2.73\t72\t32.73"/>
108 <has_text_matching expression="chr13\t107\t89.17\t16\t13.33\t0\t0.00\t16\t13.33"/>
109 <has_text_matching expression="chr17\t100\t100.00\t62\t62.00\t6\t6.00\t56\t56.00"/>
110 </assert_contents>
111 </output>
112 </test>
113 </tests>
114 <help><![CDATA[
115
116 mafCoverage is a command-line tool from the UCSC Genome Browser suite that analyses the coverage by MAF files chromosome by chromosome and genome-wide.
117
118 ]]></help>
119 <citations>
120 <citation type="bibtex">
121 @misc{mafCoverage,
122 author = {Kent UCSC},
123 title = {mafCoverage: A tool for analysing coverage by MAF files chromosome by chromosome and genome-wide},
124 note = {Tool for analysing coverage by MAF files chromosome by chromosome and genome-wide}
125 </citation>
126 </citations>
127 <creator>
128 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12" identifier="https://orcid.org/0009-0003-9935-828X"/>
129 <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
130 </creator>
131 </tool>