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1 <?xml version="1.0"?>
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2
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3 <tool id="add_names_to_bed_1" name="Add names to a BED file">
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4 <description>based on overlap with a named regions BED file</description>
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5 <version_string>echo 1.0.0</version_string>
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6 <command interpreter="perl">add_names_to_bed $in_unnamed_bed $in_named_bed $out_renamed_bed $out_log</command>
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7 <inputs>
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8 <param format="bed" name="in_unnamed_bed" type="data" label="BED file to rename" help="BED file without useful names for each region reported"/>
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9 <param format="bed" name="in_named_bed" type="data" label="BED file with names to inherit" help="BED file with useful names for each region (4th column)"/>
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10 </inputs>
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11 <outputs>
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12 <data name="out_renamed_bed" format="bed" type="data" label="BED file with renamed regions"/>
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13 <data name="out_log" format="text" type="data" label="Renaming stats"/>
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14 </outputs>
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15
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16 <tests/>
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17
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18 <help>
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19 This tool replaces names (4th column) in a BED file, based on overlap of those regions with named regions
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20 provided in another BED file. For example, a list of exome dud regions could be annotated with the gene
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21 names in the dud regions, by running this tool with the UCSC refFlat BED file as the named regions source.
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22 </help>
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23
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24 </tool>
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