Mercurial > repos > iuc > crossmap_bed

comparison crossmap_bed.xml @ 9:aa85f6cf1d16 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
author iuc
date Thu, 20 Jan 2022 04:27:28 +0000
parents c664e42e75f8
children cdb491bbf1d2
comparison
equal deleted inserted replaced
8:c664e42e75f8 9:aa85f6cf1d16
16 out.bed.unmap: invalid only 16 out.bed.unmap: invalid only
17 --> 17 -->
18 <command><![CDATA[ 18 <command><![CDATA[
19 CrossMap.py bed 19 CrossMap.py bed
20 '${chain_source.input_chain}' 20 '${chain_source.input_chain}'
21
22 '${input}' 21 '${input}'
23 22
24 #if $merge_unmapped_entries: 23 #if $merge_unmapped_entries:
25 > '${output_combined}' 24 > '${output_combined}'
26 #else: 25 #else:
27 output 26 output
27 --unmap-file output.unmap
28 #end if 28 #end if
29 29 --chromid $chromid
30 ]]></command> 30 ]]></command>
31 31
32 32
33 <inputs> 33 <inputs>
34 <param name="input" type="data" format="bed" label="BED file" 34 <param name="input" type="data" format="bed" label="BED file"
35 help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/> 35 help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
36 36
37 <expand macro="chain" /> 37 <expand macro="chain" />
38 38 <param name="chromid" type="select" label="Style of chromosome IDs">
39 <option value="a" selected="true">As-is</option>
40 <option value="l">Long style, e.g. chr1, chrX</option>
41 <option value="s">Short style, e.g. 1, X</option>
42 </param>
39 <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/> 43 <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/>
40 </inputs> 44 </inputs>
41 45
42 <outputs> 46 <outputs>
43 <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}" from_work_dir="output"> 47 <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}" from_work_dir="output">
74 <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) --> 78 <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
75 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/> 79 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
76 <param name="index_source" value="history"/> 80 <param name="index_source" value="history"/>
77 <param name="input_chain" value="aToB.over.chain" ftype="txt"/> 81 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
78 <param name="merge_unmapped_entries" value="false" /> 82 <param name="merge_unmapped_entries" value="false" />
83 <param name="chromid" value="s" />
79 84
80 <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/> 85 <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/>
81 <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/> 86 <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/>
82 </test> 87 </test>
83 <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) --> 88 <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
84 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/> 89 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
85 <param name="index_source" value="history"/> 90 <param name="index_source" value="history"/>
86 <param name="input_chain" value="aToB.over.chain" ftype="txt"/> 91 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
87 <param name="merge_unmapped_entries" value="true" /> 92 <param name="merge_unmapped_entries" value="true" />
93 <param name="chromid" value="s" />
88 94
89 <output name="output_combined" file="test_bed_02_output_a__all.bed"/> 95 <output name="output_combined" file="test_bed_02_output_a__all.bed"/>
90 </test> 96 </test>
91 97
92 <test><!-- clone of first test: tests cached reference chain file --> 98 <test><!-- clone of first test: tests cached reference chain file -->