Mercurial > repos > bgruening > deeptools

comparison bamCorrelate.xml @ 16:16310f8b24d5 draft

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Uploaded
author bgruening
date Mon, 16 Dec 2013 15:13:08 -0500
parents baf4283e2d7f
children 5ea8782d650c
comparison
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15:b96676609e10 16:16310f8b24d5
22 --fragmentLength $fragmentLength 22 --fragmentLength $fragmentLength
23 --corMethod $corMethod 23 --corMethod $corMethod
24 24
25 --plotFile $outFileName 25 --plotFile $outFileName
26 26
27 #if $outputOpt.showOutputOpt == "yes" 27 #if $output.showOutputSettings == "yes"
28 --outRawCounts '$outFileRawCounts' 28 --outRawCounts '$outFileRawCounts'
29 --outFileCorMatrix '$outFileCorMatrix' 29 --outFileCorMatrix '$outFileCorMatrix'
30 --plotFileFormat $output.outFileFormat 30 --plotFileFormat $output.outFileFormat
31 #else: 31 #else:
32 --plotFileFormat 'png' 32 --plotFileFormat 'png'
98 <expand macro="bamCorrelate_mode_actions" /> 98 <expand macro="bamCorrelate_mode_actions" />
99 </when> 99 </when>
100 100
101 </conditional> 101 </conditional>
102 102
103 <conditional name="outputOpt"> 103 <conditional name="output">
104 <param name="showOutputOpt" type="select" label="Show additional output options" > 104 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
105 <option value="no" selected="true">no</option> 105 <option value="no" selected="true">no</option>
106 <option value="yes">yes</option> 106 <option value="yes">yes</option>
107 </param> 107 </param>
108 <when value="no" /> 108 <when value="no" />
109 <when value="yes"> 109 <when value="yes">
115 115
116 </inputs> 116 </inputs>
117 <outputs> 117 <outputs>
118 <expand macro="output_image_file_format" /> 118 <expand macro="output_image_file_format" />
119 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> 119 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
120 <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveRawCounts'] == True)</filter> 120 <filter>
121 ((
122 output['showOutputSettings'] == 'yes' and
123 output['saveRawCounts'] is True
124 ))
125 </filter>
121 </data> 126 </data>
122 <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix"> 127 <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix">
123 <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveCorMatrix'] == True)</filter> 128 <filter>
129 ((
130 output['showOutputSettings'] == 'yes' and
131 output['saveCorMatrix'] is True
132 ))
133 </filter>
124 </data> 134 </data>
125 </outputs> 135 </outputs>
126 <help> 136 <help>
127 137
128 **What it does** 138 **What it does**