Mercurial > repos > iuc > ucsc_mafaddirows

comparison mafAddIRows.xml @ 0:1e64bb6893b2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
author iuc
date Thu, 05 Jun 2025 19:23:48 +0000
parents
children 76f19f4cb5e6
comparison
equal deleted inserted replaced
-1:000000000000 0:1e64bb6893b2
1 <tool id="ucsc_mafaddirows" name="mafAddIRows" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT">
2 <description>Add i rows to a MAF file</description>
3 <macros>
4 <token name="@TOOL_VERSION@">469</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">ucsc-mafaddirows</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 mafAddIRows
12 $input_maf
13 $twoBitFile
14 $output_maf
15 #if $nBeds
16 #import re
17 #for $bed in $nBeds:
18 #set identifier = re.sub('[^\s\w\-\\.]','_',str($bed.element_identifier))
19 && ln -s '$bed' '$identifier' &&
20 echo '$identifier' >> 'bed.txt'
21 #end for
22 -nBeds='bed.txt'
23 #end if
24 $addN
25 $addDash
26 ]]></command>
27 <inputs>
28 <param name="input_maf" type="data" format="maf" label="Input MAF file" help="MAF file with a single target sequence"/>
29 <param name="twoBitFile" type="data" format="twobit" label="TwoBit reference file" help="TwoBit file for the reference genome"/>
30 <param name="nBeds" type="data" format="bed" optional="true" multiple="true" label="List of BED files" help="One BED file per species with N locations"/>
31 <param name="addN" type="boolean" truevalue="-addN" falsevalue="" label="Add rows of N's" help="Add rows of N's into MAF blocks instead of annotating them"/>
32 <param name="addDash" type="boolean" truevalue="-addDash" falsevalue="" label="Add rows of -'s" help="Add rows of -'s into MAF blocks instead of annotating them"/>
33 </inputs>
34 <outputs>
35 <data name="output_maf" format="maf" label="${tool.name} on ${on_string}: MAF output"/>
36 </outputs>
37 <tests>
38 <!-- Test 1: Using -addN option -->
39 <test expect_num_outputs="1">
40 <param name="input_maf" value="mafIn.maf"/>
41 <param name="twoBitFile" value="ref.2bit"/>
42 <param name="addN" value="true"/>
43 <param name="addDash" value="false"/>
44 <output name="output_maf" ftype="maf">
45 <assert_contents>
46 <has_n_lines n="8"/>
47 <has_line line="i gorGor3.chr7 N 0 N 0"/>
48 </assert_contents>
49 </output>
50 </test>
51 <!-- Test 2: Using -addDash option -->
52 <test expect_num_outputs="1">
53 <param name="input_maf" value="mafIn.maf"/>
54 <param name="twoBitFile" value="ref.2bit"/>
55 <param name="addN" value="false"/>
56 <param name="addDash" value="true"/>
57 <output name="output_maf" ftype="maf">
58 <assert_contents>
59 <has_n_lines n="8"/>
60 <has_line line="i gorGor3.chr7 N 0 N 0"/>
61 <has_line line="s panTro4.chr7 1000 20 + 159345973 ACGTAC-TAC-TACGTACGT"/>
62 </assert_contents>
63 </output>
64 </test>
65 <!-- Test 3: -nBeds option -->
66 <test expect_num_outputs="1">
67 <param name="input_maf" value="mafIn.maf"/>
68 <param name="twoBitFile" value="ref.2bit"/>
69 <param name="nBeds" value="gorGor3.bed,hg38.bed,panTro4.bed"/>
70 <param name="addN" value="true"/>
71 <param name="addDash" value="false"/>
72 <output name="output_maf" ftype="maf">
73 <assert_contents>
74 <has_n_lines n="8"/>
75 <has_line line="i gorGor3.chr7 N 0 N 0"/>
76 </assert_contents>
77 </output>
78 </test>
79 </tests>
80 <help><![CDATA[
81 **mafAddIRows**
82
83 This tool adds 'i' rows to a Multiple Alignment Format (MAF) file. It requires a MAF file with a single target sequence.
84
85 **Usage**
86
87 - **Input MAF file**: Provide a MAF file containing alignments with only one target sequence.
88 - **TwoBit reference file**: Specify a TwoBit file for the reference genome.
89 - **List of BED files** (optional): Provide BED files (one per species) specifying N locations.
90 - **Add rows of N's**: Check to insert rows of N's into MAF blocks instead of annotating.
91 - **Add rows of -'s**: Check to insert rows of -'s into MAF blocks instead of annotating.
92
93 **Output**
94
95 - A modified MAF file with added 'i' rows or annotations based on the provided options.
96
97 **Note**
98
99 - The input MAF file must contain only a single target sequence.
100 - Use either `-addN` or `-addDash`, but not both, to modify the MAF blocks directly.
101 ]]></help>
102 <citations>
103 <citation type="bibtex">
104 @misc{mafAddIRows,
105 title = {mafAddIRows: Add 'i' rows to a MAF file},
106 author = {Kent UCSC},
107 note = {Tool for adding 'i' rows to MAF files with a single target sequence}
108 }
109 </citation>
110 </citations>
111 <creator>
112 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12"/>
113 <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
114 </creator>
115 </tool>