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comparison bamCorrelate.xml @ 10:135f3bae5c56 draft

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Uploaded
author bgruening
date Sat, 14 Dec 2013 03:29:29 -0500
parents c54d31467be4
children baf4283e2d7f
comparison
equal deleted inserted replaced
9:c53a73b8eef9 10:135f3bae5c56
1 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.1"> 1 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.2">
2 <description>correlates pairs of BAM files</description> 2 <description>correlates pairs of BAM files</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <expand macro="stdio" />
4 <macros> 5 <macros>
5 <import>deepTools_macros.xml</import> 6 <import>deepTools_macros.xml</import>
6 </macros> 7 </macros>
7 <command> 8 <command>
8 #import tempfile
9 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
10
11 #set files=[] 9 #set files=[]
12 #set labels=[] 10 #set labels=[]
13 11
14 @multiple_input_bams@ 12 @multiple_input_bams@
15 13
19 17
20 @THREADS@ 18 @THREADS@
21 19
22 --bamfiles #echo " ".join($files) 20 --bamfiles #echo " ".join($files)
23 --labels #echo " ".join($labels) 21 --labels #echo " ".join($labels)
24
25 --fragmentLength $fragmentLength 22 --fragmentLength $fragmentLength
26 --corMethod $corMethod 23 --corMethod $corMethod
27 24
28 #set newoutFileName=str($outFileName)+".png" 25 --plotFile $outFileName
29 --plotFile $newoutFileName
30 26
31 #if $outputOpt.showOutputOpt == "yes" 27 #if $outputOpt.showOutputOpt == "yes"
32 --outRawCounts '$outFileRawCounts' 28 --outRawCounts '$outFileRawCounts'
33 --outFileCorMatrix '$outFileCorMatrix' 29 --outFileCorMatrix '$outFileCorMatrix'
30 --plotFileFormat $output.outFileFormat
31 #else:
32 --plotFileFormat 'png'
34 #end if 33 #end if
35 34
36 #if $mode.modeOpt == "bins": 35 #if $mode.modeOpt == "bins":
37 --binSize '$mode.binSize' 36 --binSize '$mode.binSize'
38 --numberOfSamples '$mode.numberOfSamples' 37 --numberOfSamples '$mode.numberOfSamples'
62 --zMax $mode.advancedOpt.zMax 61 --zMax $mode.advancedOpt.zMax
63 #end if 62 #end if
64 --colorMap '$mode.advancedOpt.colorMap' 63 --colorMap '$mode.advancedOpt.colorMap'
65 64
66 #end if 65 #end if
67
68 ; mv $newoutFileName $outFileName
69 ; rm $temp_dir -rf
70 </command> 66 </command>
71 67
72 <inputs> 68 <inputs>
73 <expand macro="multiple_input_bams" /> 69 <expand macro="multiple_input_bams" />
74 70
109 <option value="no" selected="true">no</option> 105 <option value="no" selected="true">no</option>
110 <option value="yes">yes</option> 106 <option value="yes">yes</option>
111 </param> 107 </param>
112 <when value="no" /> 108 <when value="no" />
113 <when value="yes"> 109 <when value="yes">
110 <param name="outFileFormat" type="select" label="Image file format">
111 <option value="png" selected="true">png</option>
112 <option value="pdf">pdf</option>
113 <option value="svg">svg</option>
114 <option value="eps">eps</option>
115 <option value="emf">emf</option>
116 </param>
114 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/> 117 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
115 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/> 118 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
116 </when> 119 </when>
117 </conditional> 120 </conditional>
118 121
119 </inputs> 122 </inputs>
120 <outputs> 123 <outputs>
121 <data format="png" name="outFileName" /> 124 <data format="png" name="outFileName">
125 <change_format>
126 <when input="output.outFileFormat" value="pdf" format="pdf" />
127 <when input="output.outFileFormat" value="svg" format="svg" />
128 <when input="output.outFileFormat" value="eps" format="eps" />
129 <when input="output.outFileFormat" value="emf" format="emf" />
130 </change_format>
131 </data>
122 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> 132 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
123 <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveRawCounts'] == True)</filter> 133 <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveRawCounts'] == True)</filter>
124 </data> 134 </data>
125 <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix"> 135 <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix">
126 <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveCorMatrix'] == True)</filter> 136 <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveCorMatrix'] == True)</filter>