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comparison computeMatrix.xml @ 18:5ea8782d650c draft

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author bgruening
date Mon, 03 Feb 2014 13:44:35 -0500
parents b4c5dd45778a
children 8c452f37c896
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17:ef65d6b68ccc 18:5ea8782d650c
1 <tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.2"> 1 <tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.3">
2 <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description> 2 <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <expand macro="stdio" /> 4 <expand macro="stdio" />
5 <macros> 5 <macros>
6 <token name="@BINARY@">computeMatrix</token>
6 <import>deepTools_macros.xml</import> 7 <import>deepTools_macros.xml</import>
7 </macros> 8 </macros>
8 <command> 9 <command>
9 #import tempfile 10 #import tempfile
10 11
49 $mode.nanAfterEnd 50 $mode.nanAfterEnd
50 --beforeRegionStartLength $mode.beforeRegionStartLength 51 --beforeRegionStartLength $mode.beforeRegionStartLength
51 --afterRegionStartLength $mode.afterRegionStartLength 52 --afterRegionStartLength $mode.afterRegionStartLength
52 #else 53 #else
53 --regionBodyLength $mode.regionBodyLength 54 --regionBodyLength $mode.regionBodyLength
54 --startLabel $mode.startLabel 55 --startLabel "$mode.startLabel"
55 --endLabel $mode.endLabel 56 --endLabel "$mode.endLabel"
56 #if $mode.regionStartLength.regionStartLength_select == "yes": 57 #if $mode.regionStartLength.regionStartLength_select == "yes":
57 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength 58 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
58 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength 59 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
59 #end if 60 #end if
60 #end if 61 #end if
98 99
99 <when value="scale-regions" > 100 <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"/> 101 <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;." /> 102 <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)."/> 103 <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"> 104 <conditional name="regionStartLength">
104 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions"> 105 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
105 <option value="no" selected="true">no</option> 106 <option value="no" selected="true">no</option>
106 <option value="yes">yes</option> 107 <option value="yes">yes</option>
107 </param> 108 </param>
108 <when value="no" /> 109 <when value="no" />
109 <when value="yes"> 110 <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."/> 111 <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."/>
111 112 <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 <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."/> 113 </when>
113 </when> 114 </conditional>
114 </conditional>
115 </when> 115 </when>
116 116
117 <when value="reference-point"> 117 <when value="reference-point">
118 <param name="referencePoint" type="select" label="The reference point for the plotting"> 118 <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> 119 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>
206 206
207 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png 207 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
208 :alt: Relationship between computeMatrix, heatmapper and profiler 208 :alt: Relationship between computeMatrix, heatmapper and profiler
209 209
210 210
211 You can find more details in the `computeMatrix wiki`_.
212
213 .. _computeMatrix wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix
214
215
211 ----- 216 -----
212
213 .. class:: infomark
214 217
215 @REFERENCES@ 218 @REFERENCES@
216 219
217 </help> 220 </help>
218 </tool> 221 </tool>