Mercurial > repos > testtool > annotate_peak
comparison annotate_peak/annotatePeak.xml @ 18:6a9b9694acbf draft
Uploaded
author | testtool |
---|---|
date | Mon, 20 Mar 2017 06:51:22 -0400 |
parents | 54e19bceff70 |
children | 741b192da59c |
comparison
equal
deleted
inserted
replaced
17:982a01524118 | 18:6a9b9694acbf |
---|---|
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" "$annoPeakTable"</command> | 8 <command> Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoData" "$bindingType" "$upstream" "$downstream" "$ignore.peak.strand" "$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"> | |
14 <option name="human" type="text" value="EnsDb.Hsapiens.v75">Human</option> | |
15 <option name="mice" type="float" value="">Mice</option> | |
16 </param> | |
17 <param name="bindingType" type="select" display="radio" label="bindingType" help="choose bindingType"> | |
18 <option name="sS" type="text" value="startSite">startSite</option> | |
19 <option name="eS" type="text" value="endSite">endSite</option> | |
20 <option name="fR" type="text" value="fullRange">fullRange</option> | |
21 </param> | |
22 <param name="ignore.peak.strand" type="select" display="radio" label="ignore.peak.strand" help="choose TRUE or FALSE"> | |
23 <option name="T" type="text" value="TRUE">true</option> | |
24 <option name="F" type="text" value="FALSE">false</option> | |
25 </param> | |
26 <param name="upstream" type="float" value="" | |
27 label="upstream - number no bigger than 0" | |
28 help="e.g. '-5000'" > | |
29 </param> | |
30 <param name="downstream" type="float" value="" | |
31 label="downstream - number no less than 1" | |
32 help="e.g. '5000'" > | |
33 </param> | |
13 </inputs> | 34 </inputs> |
14 <outputs> | 35 <outputs> |
15 <data format="csv" name="annoPeakTable" label="peakAnno.csv"/> | 36 <data format="csv" name="annoPeakTable" label="peakAnno.csv"/> |
16 </outputs> | 37 </outputs> |
17 <tests> | 38 <tests> |