Mercurial > repos > bgruening > deeptools

comparison computeMatrix.xml @ 30:2e5b92e7f3cb draft

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Uploaded
author bgruening
date Tue, 28 Jan 2014 13:54:34 -0500
parents f996339050ac
children fc3830717e24
comparison
equal deleted inserted replaced
29:60788be7b346 30:2e5b92e7f3cb
49 $mode.nanAfterEnd 49 $mode.nanAfterEnd
50 --beforeRegionStartLength $mode.beforeRegionStartLength 50 --beforeRegionStartLength $mode.beforeRegionStartLength
51 --afterRegionStartLength $mode.afterRegionStartLength 51 --afterRegionStartLength $mode.afterRegionStartLength
52 #else 52 #else
53 --regionBodyLength $mode.regionBodyLength 53 --regionBodyLength $mode.regionBodyLength
54 --startLabel $mode.startLabel 54 --startLabel "$mode.startLabel"
55 --endLabel $mode.endLabel 55 --endLabel "$mode.endLabel"
56 #if $mode.regionStartLength.regionStartLength_select == "yes": 56 #if $mode.regionStartLength.regionStartLength_select == "yes":
57 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength 57 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
58 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength 58 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
59 #end if 59 #end if
60 #end if 60 #end if
98 98
99 <when value="scale-regions" > 99 <when value="scale-regions" >
100 <param name="regionBodyLength" type="integer" value="500" label="Distance in bp to which all regions are going to be fitted"/> 100 <param name="regionBodyLength" type="integer" value="500" label="Distance in bp to which all regions are going to be fitted"/>
101 <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" help ="Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." /> 101 <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" help ="Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
102 <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" help="Label shown in the plot for the region end. Default is TES (transcription end site)."/> 102 <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" help="Label shown in the plot for the region end. Default is TES (transcription end site)."/>
103 <conditional name="regionStartLength"> 103 <conditional name="regionStartLength">
104 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions"> 104 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
105 <option value="no" selected="true">no</option> 105 <option value="no" selected="true">no</option>
106 <option value="yes">yes</option> 106 <option value="yes">yes</option>
107 </param> 107 </param>
108 <when value="no" /> 108 <when value="no" />
109 <when value="yes"> 109 <when value="yes">
110 <param name="beforeRegionStartLength" type="integer" value="1000" min="1" optional="true" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/> 110 <param name="beforeRegionStartLength" type="integer" value="1000" min="1" optional="true" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/>
111 111 <param name="afterRegionStartLength" type="integer" value="1000" min="1" optional="true" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/>
112 <param name="afterRegionStartLength" type="integer" value="1000" min="1" optional="true" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/> 112 </when>
113 </when> 113 </conditional>
114 </conditional>
115 </when> 114 </when>
116 115
117 <when value="reference-point"> 116 <when value="reference-point">
118 <param name="referencePoint" type="select" label="The reference point for the plotting"> 117 <param name="referencePoint" type="select" label="The reference point for the plotting">
119 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option> 118 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>