Mercurial > repos > bgruening > deeptools_plot_coverage

comparison plotCoverage.xml @ 36:2c17ceeae363 draft

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"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
author bgruening
date Fri, 24 Jan 2020 07:40:30 +0000
parents f0511595bbd3
children 18ef8e2c9763
comparison
equal deleted inserted replaced
35:ed617a38a03e 36:2c17ceeae363
23 23
24 #if $outRawCounts: 24 #if $outRawCounts:
25 --outRawCounts '$outFileRawCounts' 25 --outRawCounts '$outFileRawCounts'
26 #end if 26 #end if
27 27
28 #if ' '.join(map(str, $BED)) != 'None':
29 #set bedFileLList=[]
30 #for $f in $BED:
31 #silent $bedFileList.append("'%s'" % $f)
32 #end for
33 #if $bedFileList != ["'None'"]:
34 --BED #echo ' '.join($bedFileList)#
35 #end if
36 #end if
37
38 #if $coverageOpt.showCoverageOpt == "yes":
39 --outCoverageMetrics '$outFileCoverageMetrics'
40 #for $t in $coverageOpt.thresholds:
41 -ct $t.coverageThreshold
42 #end for
43 #end if
44
28 #if $advancedOpt.showAdvancedOpt == "yes": 45 #if $advancedOpt.showAdvancedOpt == "yes":
29 --numberOfSamples '$advancedOpt.numberOfSamples' 46 --numberOfSamples '$advancedOpt.numberOfSamples'
30 $advancedOpt.skipZeros 47 $advancedOpt.skipZeros
31 48
32 #if str($advancedOpt.region).strip() != '': 49 #if str($advancedOpt.region).strip() != '':
46 </command> 63 </command>
47 <inputs> 64 <inputs>
48 65
49 <expand macro="multiple_input_bams" MIN="1"/> 66 <expand macro="multiple_input_bams" MIN="1"/>
50 <expand macro="custom_sample_labels" /> 67 <expand macro="custom_sample_labels" />
68 <param argument="--BED" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
69 label="Regions of interest"
70 help="Limits the coverage analysis to the regions specified in these files. This overrides --numberOfSamples. It is inadvisable to combine this with saving the raw counts." />
71
72 <conditional name="coverageOpt">
73 <param name="showCoverageOpt" type="select" label="Show coverage metrics options">
74 <option value="no" selected="true">No</option>
75 <option value="yes">Yes</option>
76 </param>
77 <when value="no" />
78 <when value="yes">
79 <param argument="--outCoverageMetrics" type="boolean" label="Save per-threshold coverage metrics?"/>
80 <repeat name="thresholds" title="Coverage Thresholds">
81 <param argument="--coverageThreshold" type="integer" min="0" label="Coverage Threshold" value="0"/>
82 </repeat>
83 </when>
84 </conditional>
51 85
52 <conditional name="advancedOpt"> 86 <conditional name="advancedOpt">
53 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 87 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
54 <option value="no" selected="true">no</option> 88 <option value="no" selected="true">No</option>
55 <option value="yes">yes</option> 89 <option value="yes">Yes</option>
56 </param> 90 </param>
57 <when value="no" /> 91 <when value="no" />
58 <when value="yes"> 92 <when value="yes">
59 <param argument="--numberOfSamples" type="integer" value="100000" min="1" 93 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
60 label="Number of samples" 94 label="Number of samples"
76 <outputs> 110 <outputs>
77 <expand macro="output_image_file_format_not_nested" /> 111 <expand macro="output_image_file_format_not_nested" />
78 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> 112 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
79 <filter>outRawCounts is True</filter> 113 <filter>outRawCounts is True</filter>
80 </data> 114 </data>
115 <data format="tabular" name="outFileCoverageMetrics" label="${tool.name} on ${on_string}: Threshold Metrics">
116 <filter>coverageOpt.outCoverageMetrics is True</filter>
117 </data>
81 </outputs> 118 </outputs>
82 <tests> 119 <tests>
83 <test> 120 <test>
84 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" /> 121 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
85 <!--param name="outFileFormat" value="png" /--> 122 <!--param name="outFileFormat" value="png" /-->
86 <param name="showAdvancedOpt" value="yes" /> 123 <param name="showAdvancedOpt" value="yes" />
87 <param name="plotTitle" value="Test Title from Galaxy" /> 124 <param name="plotTitle" value="Test Title from Galaxy" />
88 <param name="outRawCounts" value="True" /> 125 <param name="outRawCounts" value="True" />
89 <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" /> 126 <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
90 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" /> 127 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
128 </test>
129 <test>
130 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
131 <param name="showAdvancedOpt" value="yes" />
132 <param name="plotTitle" value="Test Title from Galaxy" />
133 <param name="showCoverageOpt" value="yes" />
134 <param name="coverageThreshold" value="0" />
135 <param name="coverageThreshold" value="5" />
136 <param name="coverageThreshold" value="10" />
137 <param name="coverageThreshold" value="20" />
138 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
139 <output name="outFileCoverageMetrics" file="plotCoverage.metrics" ftype="tabular" />
91 </test> 140 </test>
92 </tests> 141 </tests>
93 <help> 142 <help>
94 <![CDATA[ 143 <![CDATA[
95 What it does 144 What it does