Mercurial > repos > iuc > crossmap_bed

comparison crossmap_bed.xml @ 4:aebc86cb895d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
author iuc
date Thu, 24 May 2018 19:08:41 -0400
parents e5c951338c64
children c664e42e75f8
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3:e5c951338c64 4:aebc86cb895d
1 <tool id="crossmap_bed" name="CrossMap BED" version="@WRAPPER_VERSION@-0"> 1 <tool id="crossmap_bed" name="CrossMap BED" version="@WRAPPER_VERSION@">
2 <description>Convert genome coordinates or annotation files between genome assemblies</description> 2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
22 '${input}' 22 '${input}'
23 23
24 #if $merge_unmapped_entries: 24 #if $merge_unmapped_entries:
25 > '${output_combined}' 25 > '${output_combined}'
26 #else: 26 #else:
27 '${output_valid}' 27 output
28 && mv '${output_valid}.unmap' '${output_failed}'
29 #end if 28 #end if
30 29
31 ]]></command> 30 ]]></command>
32 31
33 32
39 38
40 <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/> 39 <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/>
41 </inputs> 40 </inputs>
42 41
43 <outputs> 42 <outputs>
44 <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}"> 43 <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}" from_work_dir="output">
45 <filter>merge_unmapped_entries is False</filter> 44 <filter>merge_unmapped_entries is False</filter>
46 </data> 45 </data>
47 <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}"> 46 <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}" from_work_dir="output.unmap">
48 <filter>merge_unmapped_entries is False</filter> 47 <filter>merge_unmapped_entries is False</filter>
49 </data> 48 </data>
50 49
51 <data name="output_combined" format="bed" label="${tool.name} on ${on_string}"> 50 <data name="output_combined" format="bed" label="${tool.name} on ${on_string}">
52 <filter>merge_unmapped_entries is True</filter> 51 <filter>merge_unmapped_entries is True</filter>
133 6. For standard BED format (12 columns). If any of the defined exon blocks 132 6. For standard BED format (12 columns). If any of the defined exon blocks
134 cannot be uniquely mapped to target assembly, the whole entry will be 133 cannot be uniquely mapped to target assembly, the whole entry will be
135 skipped. 134 skipped.
136 7. If input region cannot be consecutively mapped target assembly, it will be split. 135 7. If input region cannot be consecutively mapped target assembly, it will be split.
137 8. \*.unmap file contains regions that cannot be unambiguously converted. 136 8. \*.unmap file contains regions that cannot be unambiguously converted.
138
139 ]]></help> 137 ]]></help>
140 138
141 <citations> 139 <citations>
142 <citation type="doi">10.1093/bioinformatics/btt730</citation> 140 <citation type="doi">10.1093/bioinformatics/btt730</citation>
143 </citations> 141 </citations>