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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="2014-09-16">cistrome</requirement>
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5 <requirement type="package" version="2.15.0">R</requirement>
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6 <requirement type="package" version="0.7.1">bx-python</requirement>
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7 </requirements>
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8 </xml>
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9 <xml name="requirements_union">
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10 <requirements>
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11 <requirement type="package" version="2014-09-16">cistrome</requirement>
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12 <requirement type="package" version="2.15.0">R</requirement>
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13 <requirement type="package" version="1.36.0">bioc_geneplotter</requirement>
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14 </requirements>
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15 </xml>
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16 <xml name="stdio">
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17 <stdio>
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18 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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19 <exit_code range="1:" level="fatal" description="Error" />
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20 </stdio>
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21 </xml>
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22 <xml name="commom_params">
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23 <param format="wig,bigwig" name="wfile1" type="data" label="Wiggle / bigwig file 1">
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24 <validator type="unspecified_build" />
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25 </param>
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26 <param name="wlabel1" type="text" label="Wiggle / bigwig label 1" optional="false">
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27 <validator type="length" message="must be between 1 and 255 characters" min="1" max="255"/>
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28 </param>
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29 <param format="wig,bigwig" name="wfile2" type="data" label="Wiggle / bigwig file 2">
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30 <validator type="unspecified_build" />
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31 </param>
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32 <param name="wlabel2" type="text" label="Wiggle / bigwig label 2" optional="false">
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33 <validator type="length" message="must be between 1 and 255 characters" min="1" max="255"/>
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34 </param>
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35 <repeat name="more" title="wiggle / bigwig file">
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36 <param format="wig,bigwig" name="wig" type="data" label="Select another wiggle / bigwig file"/>
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37 <param name="label" type="text" label="Wiggle / bigwig label" optional="false">
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38 <validator type="length" message="must be between 1 and 255 characters" min="1" max="255"/>
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39 </param>
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40 </repeat>
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41 <param name="method" type="select" label="method:" help="method to process the paired two sets of data in the sampling step." >
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42 <option value="mean" selected="true">mean</option>
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43 <option value="median">median</option>
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44 <option value="sample">sample</option>
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45 </param>
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46 <param name="maxscore" type="float" label="Max Score" help="Maximum score in the calculation (optional)" value="10000" optional="true"/>
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47 <param name="minscore" type="float" label="Min Score" help="Minimum score in the calculation (optional)" value="-10000" optional="true"/>
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48 <param name="heatmap" type="boolean" label="Draw Heatmap instead?" checked="no"
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49 truevalue="-H" falsevalue=" " />
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50 <param name="size" type="integer" label="image Size" value="10" help="Image size in inch. It must be ge 5 and le 20. Default: 10">
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51 <validator type="in_range" max="20" min="5" message="image Size is out of range, image Size has to be between 5 to 20" />
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52 </param>
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53 <param type="select" name="imagetype" display="radio" label="Image Type">
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54 <option value="PDF">PDF format</option>
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55 <option value="PNG">PNG format</option>
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56 </param>
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57 </xml>
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58
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59 <template name="script_chars">
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60 #set global $dollar = chr(36)
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61 #set global $gt = chr(62)
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62 #set global $lt = chr(60)
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63 #set global $ad = chr(38)
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64 </template>
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65
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66 <token name="@EXTERNAL_DOCUMENTATION@">
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67
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68 For details about this application, please go to:
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69 https://bitbucket.org/cistrome/cistrome-harvard/wiki/Home
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70
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71 </token>
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72 <token name="@CITATION_SECTION@">------
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73
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74 **Citation**
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75
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76 For the underlying tool, please cite the following publication:
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77 "Cistrome: an integrative platform for transcriptional regulation studies," Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XS. Genome Biol. 2011 Aug 22;12(8):R83.
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78
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79 </token>
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80 </macros>
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