Mercurial > repos > xiaoyi-cao > annotatebed

comparison annotateBedWrapper.xml @ 9:6935cb1ed000 draft default tip

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author xiaoyi-cao
date Sun, 02 Dec 2012 15:37:32 -0500
parents 57a9a34af5ce
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8:57a9a34af5ce 9:6935cb1ed000
1 <tool id="annotateBed" name="annotateBed"> 1 <tool id="annotateBed" name="Annotates">
2 2
3 <description>Annotate BED files with overlapping BED files</description> 3 <description> the depth & breadth of coverage of features from multiple files</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="binary">annotateBed</requirement> 6 <requirement type="binary">annotateBed</requirement>
7 <requirement type="package">bedtools</requirement> 7 <requirement type="package">bedtools</requirement>
8 </requirements> 8 </requirements>
9 9
22 &gt; '$output' 22 &gt; '$output'
23 </command> 23 </command>
24 24
25 <inputs> 25 <inputs>
26 26
27 <param name="countflag" type="boolean" label="Use count to annotate" truevalue="-count" falsevalue="" /> 27 <param format="bed" name="inputRegion" type="data" label="The regions to be annotated is in this file:" />
28 <param format="bed" name="inputRegion" type="data" label="The region to be annotated" /> 28 <param name="countflag" type="select" label="What to report in the output: ">
29 <option value="-counts" selected="true">the count of features in each file that overlap the regions</option>
30 <option value="">fraction of the region covered by each feature</option>
31 <option value="-both">Report the counts followed by the % coverage</option>
32 </param>
29 <repeat name="annotateColumn" title="Column"> 33 <repeat name="annotateColumn" title="Column">
30 <param name="colname" type="text" label="Column name" /> 34 <param name="colname" type="text" label="Feature name" />
31 <param name="colfile" type="data" format="bed" label="BED file to annotate for the column" /> 35 <param name="colfile" type="data" format="bed" label="Feature file to annotate for the column" />
32 </repeat> 36 </repeat>
33 37
34 </inputs> 38 </inputs>
35 <outputs> 39 <outputs>
36 <data format="bed" name="output" metadata_source="inputRegion" label="${inputRegion.name} annotated" /> 40 <data format="bed" name="output" label="${inputRegion.name} annotated" />
37 </outputs> 41 </outputs>
38 42
39 <help> 43 <help>
40 44
41 .. class:: infomark 45 **What it does**
42 46
43 IMPORTANT INFORMATION 47 This tool is used to annotate the regions in a bed file with features provided in multiple BED files.
44 48
45 ---- 49 ..class:: warningmark
46 50
47 WRITE HELP HERE 51 This tool requires that bedtools__ has been installed on your system.
52
53 -----
48 54
49 </help> 55 </help>
50 56
51 </tool> 57 </tool>