Mercurial > repos > testtool > annotate_peak
comparison annotate_peak/annotatePeak.xml @ 19:741b192da59c draft
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author | testtool |
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date | Mon, 20 Mar 2017 07:19:42 -0400 |
parents | 6a9b9694acbf |
children | 2044ad2c1c93 |
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18:6a9b9694acbf | 19:741b192da59c |
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3 <requirement type="package" version="3.2.1">R</requirement> | 3 <requirement type="package" version="3.2.1">R</requirement> |
4 </requirements> | 4 </requirements> |
5 <stdio> | 5 <stdio> |
6 <exit_code range="1:" /> | 6 <exit_code range="1:" /> |
7 </stdio> | 7 </stdio> |
8 <command> Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoData" "$bindingType" "$upstream" "$downstream" "$ignore.peak.strand" "$annoPeakTable"</command> | 8 <command> Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoData" "$bindingType" "$upstream" "$downstream" "$ignore" "$annoPeakTable"</command> |
9 <inputs> | 9 <inputs> |
10 <param optional="false" format="bed" name="DMR" type="data" value="" help="Bumphunter peaks." label="[required] file"> | 10 <param optional="false" format="bed" name="DMR" type="data" value="" help="Bumphunter peaks." label="[required] file"> |
11 <validator type="empty_field" message="This field is required."/> | 11 <validator type="empty_field" message="This field is required."/> |
12 </param> | 12 </param> |
13 <param name="annoData" type="select" display="radio" label="annoData" help="choose your annoData human or mice"> | 13 <param name="annoData" type="select" label="annoData" help="choose your annoData human or mice"> |
14 <option name="human" type="text" value="EnsDb.Hsapiens.v75">Human</option> | 14 <option name="human" type="text" value="EnsDb.Hsapiens.v75">Human</option> |
15 <option name="mice" type="float" value="">Mice</option> | 15 <option name="mice" type="float" value="">Mice</option> |
16 </param> | 16 </param> |
17 <param name="bindingType" type="select" display="radio" label="bindingType" help="choose bindingType"> | 17 <param name="bindingType" type="select" label="bindingType" help="choose bindingType"> |
18 <option name="sS" type="text" value="startSite">startSite</option> | 18 <option name="sS" type="text" value="startSite">startSite</option> |
19 <option name="eS" type="text" value="endSite">endSite</option> | 19 <option name="eS" type="text" value="endSite">endSite</option> |
20 <option name="fR" type="text" value="fullRange">fullRange</option> | 20 <option name="fR" type="text" value="fullRange">fullRange</option> |
21 </param> | 21 </param> |
22 <param name="ignore.peak.strand" type="select" display="radio" label="ignore.peak.strand" help="choose TRUE or FALSE"> | 22 <param name="ignore" type="select" label="ignore.peak.strand" help="choose TRUE or FALSE"> |
23 <option name="T" type="text" value="TRUE">true</option> | 23 <option name="T" type="text" value="TRUE">true</option> |
24 <option name="F" type="text" value="FALSE">false</option> | 24 <option name="F" type="text" value="FALSE">false</option> |
25 </param> | 25 </param> |
26 <param name="upstream" type="float" value="" | 26 <param name="upstream" type="text" value="" |
27 label="upstream - number no bigger than 0" | 27 label="upstream - number no bigger than 0" |
28 help="e.g. '-5000'" > | 28 help="e.g. '-5000'" > |
29 </param> | 29 </param> |
30 <param name="downstream" type="float" value="" | 30 <param name="downstream" type="text" value="" |
31 label="downstream - number no less than 1" | 31 label="downstream - number no less than 1" |
32 help="e.g. '5000'" > | 32 help="e.g. '5000'" > |
33 </param> | 33 </param> |
34 </inputs> | 34 </inputs> |
35 <outputs> | 35 <outputs> |
36 <data format="csv" name="annoPeakTable" label="peakAnno.csv"/> | 36 <data format="txt" name="annoPeakTable" label="peakAnno.txt"/> |
37 </outputs> | 37 </outputs> |
38 <tests> | 38 <tests> |
39 <test> | 39 <test> |
40 <param name="test"> | 40 <param name="test"> |
41 <element name="test-data"> | 41 <element name="test-data"> |
42 <collection type="data"> | 42 <collection type="data"> |
43 <element name="DMR" value="test-data/DMR.bed"/> | 43 <element name="DMR" value="test-data/DMR.bed"/> |
44 </collection> | 44 </collection> |
45 </element> | 45 </element> |
46 </param> | 46 </param> |
47 <output format="csv" name="annoPeakTable" label="test-data/annoPeakTable.csv"/> | 47 <output format="txt" name="annoPeakTable" label="test-data/annoPeakTable.txt"/> |
48 </test> | 48 </test> |
49 </tests> | 49 </tests> |
50 <help> | 50 <help> |
51 **Description** | 51 **Description** |
52 </help> | 52 </help> |