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comparison crossmap_region.xml @ 0:8635b6b8a8f2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
author iuc
date Thu, 15 Jul 2021 16:19:33 +0000
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-1:000000000000 0:8635b6b8a8f2
1 <tool id="crossmap_region" name="CrossMap region" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 CrossMap.py region
11 '${chain_source.input_chain}'
12 '${input}'
13 --ratio $ratio
14 '$output'
15 ]]></command>
16 <inputs>
17 <param name="input" type="data" format="bed" label="BED file"
18 help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
19 <expand macro="chain" />
20 <param argument="--ratio" type="float" min="0" max="1" value="0.85" label="Minimum ratio of bases that must remap."/>
21 </inputs>
22 <outputs>
23 <data name="output" format="bed"/>
24 </outputs>
25 <tests>
26 <test>
27 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
28 <param name="index_source" value="history"/>
29 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
30 <output name="output" file="test_region.bed"/>
31 </test>
32 </tests>
33 <help><![CDATA[
34 @HELP_GENERAL@
35
36 CrossMap region
37 ---------------
38
39 Unlike the "CrossMap bed" function which splits big genomic regions, "CrossMap region" tries to convert the big genomic region as a whole.
40
41 BED
42 ---
43
44 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
45 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
46
47 A BED (Browser Extensible Data) file is a tab-delimited text file
48 describing genome regions or gene annotations. It is the standard file
49 format used by UCSC. It consists of one line per feature, each containing
50 3-12 columns. CrossMap converts BED files with less than 12 columns to a
51 different assembly by updating the chromosome and genome coordinates only;
52 all other columns remain unchanged. Regions from old assembly mapping to
53 multiple locations to the new assembly will be split. For 12-columns BED
54 files, all columns will be updated accordingly except the 4th column (name
55 of bed line), 5th column (score value) and 9th column (RGB value describing
56 the display color). 12-column BED files usually define multiple blocks (eg.
57 exon); if any of the exons fails to map to a new assembly, the whole BED
58 line is skipped.
59
60 Notes:
61
62 1. For BED-like formats mentioned above, CrossMap only updates “chrom (1st
63 column)”, “start (2nd column) ”, “end (3rd column) ” and “strand” (if
64 any). All other columns will keep AS-IS.
65 2. Lines starting with ‘#’, ‘browser’, ‘track’ will be skipped.
66 3. Lines will less than 3 columns will be skipped.
67 4. 2nd-column and 3-column must be integer, otherwise skipped.
68 5. “+” strand is assumed if no strand information was found.
69 6. For standard BED format (12 columns). If any of the defined exon blocks
70 cannot be uniquely mapped to target assembly, the whole entry will be
71 skipped.
72 7. If input region cannot be consecutively mapped target assembly, it will be split.
73 8. \*.unmap file contains regions that cannot be unambiguously converted.
74 ]]></help>
75
76 <citations>
77 <citation type="doi">10.1093/bioinformatics/btt730</citation>
78 </citations>
79 </tool>