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comparison bamFingerprint.xml @ 13:b4c5dd45778a draft

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Uploaded
author bgruening
date Mon, 16 Dec 2013 04:36:19 -0500
parents 135f3bae5c56
children 16310f8b24d5
comparison
equal deleted inserted replaced
12:aea72b24dea0 13:b4c5dd45778a
24 --fragmentLength $fragmentLength 24 --fragmentLength $fragmentLength
25 25
26 #set newoutFileName=str($outFileName)+".png" 26 #set newoutFileName=str($outFileName)+".png"
27 --plotFile $newoutFileName 27 --plotFile $newoutFileName
28 28
29 #if $outputOpt.showOutputOpt == "yes" 29 #if $output.showOutputSettings == "yes"
30 #if $outputOpt.saveRawCounts: 30 --plotFileFormat $output.outFileFormat
31 #if $output.saveRawCounts:
31 --outRawCounts '$outFileRawCounts' 32 --outRawCounts '$outFileRawCounts'
32 #end if 33 #end if
34 #else
35 --plotFileFormat 'png'
33 #end if 36 #end if
37
34 38
35 #if $advancedOpt.showAdvancedOpt == "yes": 39 #if $advancedOpt.showAdvancedOpt == "yes":
36 40
37 #if str($advancedOpt.region.value) != '': 41 #if str($advancedOpt.region.value) != '':
38 --region '$advancedOpt.region' 42 --region '$advancedOpt.region'
93 label ="Include zeros" 97 label ="Include zeros"
94 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined." /> 98 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined." />
95 </when> 99 </when>
96 </conditional> 100 </conditional>
97 101
98 <conditional name="outputOpt"> 102 <conditional name="output">
99 <param name="showOutputOpt" type="select" label="Show additional output options" > 103 <param name="showOutputSettings" type="select" label="Show advanced output settings">
100 <option value="no" selected="true">no</option> 104 <option value="no" selected="true">no</option>
101 <option value="yes">yes</option> 105 <option value="yes">yes</option>
102 </param> 106 </param>
103 <when value="no" /> 107 <when value="no" />
104 <when value="yes"> 108 <when value="yes">
109 <expand macro="input_image_file_format" />
105 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/> 110 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
106 </when> 111 </when>
107 </conditional> 112 </conditional>
108 113
109 </inputs> 114 </inputs>
110 <outputs> 115 <outputs>
111 <data format="png" name="outFileName" /> 116 <expand macro="output_image_file_format" />
112 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> 117 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
113 <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveRawCounts'] == True)</filter> 118 <filter>
119 ((
120 outputOpt['showOutputOpt'] == 'yes' and
121 outputOpt['saveRawCounts'] is True
122 ))
123 </filter>
114 </data> 124 </data>
115 </outputs> 125 </outputs>
116 <help> 126 <help>
117 127
118 **What it does** 128 **What it does**