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comparison crossmap_bed.xml @ 0:235ab3277db1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
author iuc
date Sat, 01 Jul 2017 17:44:51 -0400
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-1:000000000000 0:235ab3277db1
1 <tool id="crossmap_bed" name="CrossMap BED" version="@WRAPPER_VERSION@-0">
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
10 <command><![CDATA[
11 #set $input_file = str($seq_source.input)
12
13 CrossMap.py bed
14 '${chain_source.input_chain}'
15
16 '${input_file}'
17
18 #if str($include_fails) == "True"
19 >
20 #end if
21
22 '${output}'
23 ]]></command>
24
25
26 <inputs>
27 <conditional name="seq_source">
28 <expand macro="source" />
29
30 <when value="cached">
31 <param format="bed" name="input" type="data" label="BED file"
32 help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.">
33 <validator type="unspecified_build"/>
34 <!-- Gives error in tests
35 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
36 -->
37 </param>
38 </when>
39 <when value="history">
40 <param type="data" format="bed" name="input" label="BED file"
41 help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns."/>
42 </when>
43 </conditional>
44 <expand macro="chain" />
45
46 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers"
47 help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
48 </inputs>
49
50 <outputs>
51 <data format="bed" name="output" label="${tool.name} on ${on_string}" />
52 <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}" />
53 </outputs>
54
55 <tests>
56 <!-- BED -->
57 <test>
58 <param name="index_source" value="history"/>
59 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
60 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
61 <param name="include_fails" value="False"/>
62
63 <output name="output" file="test_bed_01_output_a__only-matches.bed"/>
64 </test>
65 <test>
66 <param name="index_source" value="history"/>
67 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
68 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
69 <param name="include_fails" value="True"/>
70
71 <output name="output" file="test_bed_01_output_a__all.bed"/>
72 </test>
73 <test>
74 <param name="index_source" value="history"/>
75 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
76 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
77 <param name="include_fails" value="False"/>
78
79 <output name="output" file="test_bed_02_output_a__only-matches.bed"/>
80 </test>
81 <test>
82 <param name="index_source" value="history"/>
83 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
84 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
85 <param name="include_fails" value="True"/>
86
87 <output name="output" file="test_bed_02_output_a__all.bed"/>
88 </test>
89 </tests>
90 <help><![CDATA[
91 @HELP_GENERAL@
92
93 BED
94 ---
95
96 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
97 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
98
99 A BED (Browser Extensible Data) file is a tab-delimited text file
100 describing genome regions or gene annotations. It is the standard file
101 format used by UCSC. It consists of one line per feature, each containing
102 3-12 columns. CrossMap converts BED files with less than 12 columns to a
103 different assembly by updating the chromosome and genome coordinates only;
104 all other columns remain unchanged. Regions from old assembly mapping to
105 multiple locations to the new assembly will be split. For 12-columns BED
106 files, all columns will be updated accordingly except the 4th column (name
107 of bed line), 5th column (score value) and 9th column (RGB value describing
108 the display color). 12-column BED files usually define multiple blocks (eg.
109 exon); if any of the exons fails to map to a new assembly, the whole BED
110 line is skipped.
111
112 NOTE:
113
114 1. For BED-like formats mentioned above, CrossMap only updates “chrom (1st
115 column)”, “start (2nd column) ”, “end (3rd column) ” and “strand” (if
116 any). All other columns will keep AS-IS.
117 2. Lines starting with ‘#’, ‘browser’, ‘track’ will be skipped.
118 3. Lines will less than 3 columns will be skipped.
119 4. 2nd-column and 3-column must be integer, otherwise skipped.
120 5. “+” strand is assumed if no strand information was found.
121 6. For standard BED format (12 columns). If any of the defined exon blocks
122 cannot be uniquely mapped to target assembly, the whole entry will be
123 skipped.
124 7. If input region cannot be consecutively mapped target assembly, it will be split.
125 8. *.unmap file contains regions that cannot be unambiguously converted.
126
127 Please see `the manual <http://crossmap.sourceforge.net/#convert-bed-format-files>`__ for more details.
128 ]]></help>
129
130 <citations>
131 <citation type="doi">10.1093/bioinformatics/btt730</citation>
132 </citations>
133 </tool>