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comparison crossmap_region.xml @ 2:a50ef4d58c90 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author iuc
date Mon, 02 Sep 2024 12:01:39 +0000
parents eb66d7a04bf8
children
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1:eb66d7a04bf8 2:a50ef4d58c90
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 CrossMap.py region 10 CrossMap region
11 '${chain_source.input_chain}' 11 '${chain_source.input_chain}'
12 '${input}' 12 '${input}'
13 $output 13 $output
14 --chromid $chromid 14 --chromid $chromid
15 --ratio $ratio 15 --ratio $ratio
16 ]]></command> 16 ]]></command>
17 <inputs> 17 <inputs>
18 <param name="input" type="data" format="bed" label="BED file" 18 <param name="input" type="data" format="bed" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
19 help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/> 19 <expand macro="chain"/>
20 <expand macro="chain" />
21 <param argument="--ratio" type="float" min="0" max="1" value="0.85" label="Minimum ratio of bases that must remap."/> 20 <param argument="--ratio" type="float" min="0" max="1" value="0.85" label="Minimum ratio of bases that must remap."/>
22 <param argument="--chromid" type="select" label="Chromid" help="The style of chromosome IDs"> 21 <param argument="--chromid" type="select" label="Chromid" help="The style of chromosome IDs">
23 <option value="a" selected="true">Default (a)</option> 22 <option value="a" selected="true">Default (a)</option>
24 <option value="s">Short style (s)</option> 23 <option value="s">Short style (s)</option>
25 <option value="l">Long stype (l)</option> 24 <option value="l">Long stype (l)</option>
76 cannot be uniquely mapped to target assembly, the whole entry will be 75 cannot be uniquely mapped to target assembly, the whole entry will be
77 skipped. 76 skipped.
78 7. If input region cannot be consecutively mapped target assembly, it will be split. 77 7. If input region cannot be consecutively mapped target assembly, it will be split.
79 8. \*.unmap file contains regions that cannot be unambiguously converted. 78 8. \*.unmap file contains regions that cannot be unambiguously converted.
80 ]]></help> 79 ]]></help>
81
82 <citations> 80 <citations>
83 <citation type="doi">10.1093/bioinformatics/btt730</citation> 81 <citation type="doi">10.1093/bioinformatics/btt730</citation>
84 </citations> 82 </citations>
85 </tool> 83 </tool>