Mercurial > repos > bgruening > deeptools_compute_matrix

comparison computeMatrix.xml @ 3:a842285199d9 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
author bgruening
date Wed, 09 Mar 2016 18:33:21 -0500
parents 275ed3e83de0
children aee77c22123d
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2:df1ee352b23b 3:a842285199d9
49 #else 49 #else
50 --regionBodyLength $mode.regionBodyLength 50 --regionBodyLength $mode.regionBodyLength
51 #if $mode.regionStartLength.regionStartLength_select == "yes": 51 #if $mode.regionStartLength.regionStartLength_select == "yes":
52 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength 52 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
53 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength 53 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
54 #end if 54
55 --unscaled5prime $mode.regionStartLength.unscaled5prime
56 --unscaled3prime $mode.regionStartLength.unscaled3prime
57
58 #end if
59
55 #end if 60 #end if
56 61
57 #if $advancedOpt.showAdvancedOpt == "yes": 62 #if $advancedOpt.showAdvancedOpt == "yes":
58 --sortRegions '$advancedOpt.sortRegions' 63 --sortRegions '$advancedOpt.sortRegions'
59 --sortUsing '$advancedOpt.sortUsing' 64 --sortUsing '$advancedOpt.sortUsing'
69 --maxThreshold $advancedOpt.maxThreshold 74 --maxThreshold $advancedOpt.maxThreshold
70 #end if 75 #end if
71 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '': 76 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
72 --scale $advancedOpt.scale 77 --scale $advancedOpt.scale
73 #end if 78 #end if
74
75 #end if 79 #end if
76 ]]> 80 ]]>
77 </command> 81 </command>
78 <inputs> 82 <inputs>
79 83
116 distance upstream of the transcription start site."/> 120 distance upstream of the transcription start site."/>
117 <param argument="--afterRegionStartLength" type="integer" value="1000" min="1" 121 <param argument="--afterRegionStartLength" type="integer" value="1000" min="1"
118 label="Distance downstream of the region end position" 122 label="Distance downstream of the region end position"
119 help="If the regions are genes, this would be the 123 help="If the regions are genes, this would be the
120 distance downstream of the transcription end site."/> 124 distance downstream of the transcription end site."/>
125 <param argument="--unscaled5prime" type="integer" min="0" value="0"
126 label="Number of bases within the gene body at the 5-prime end to exclude from scaling."
127 help="By default, each region is scaled to a given length (see the --regionBodyLength
128 option). In some cases it is useful to look at unscaled signals around region boundaries, so this
129 setting specifies the number of unscaled bases on the 5-prime end of each boundary." />
130 <param argument="--unscaled3prime" type="integer" min="0" value="0"
131 label="Number of bases within the gene body at the 3-prime end to exclude from scaling."
132 help="As with --unscaled5prime, but for the 3-prime end." />
121 </when> 133 </when>
122 </conditional> 134 </conditional>
123 </when> 135 </when>
124 <when value="reference-point"> 136 <when value="reference-point">
125 <param name="referencePoint" type="select" label="The reference point for the plotting"> 137 <param name="referencePoint" type="select" label="The reference point for the plotting">
200 <outputs> 212 <outputs>
201 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> 213 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
202 <expand macro="output_graphic_outputs" /> 214 <expand macro="output_graphic_outputs" />
203 <expand macro="output_save_matrix_values" /> 215 <expand macro="output_save_matrix_values" />
204 </outputs> 216 </outputs>
205 <!--
206 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
207 -->
208 <tests> 217 <tests>
209 <test> 218 <test>
210 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" /> 219 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
211 <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" /> 220 <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" />
212 <param name="showAdvancedOpt" value="yes" /> 221 <param name="showAdvancedOpt" value="yes" />