Mercurial > repos > bgruening > deeptools_plot_coverage

comparison plotCoverage.xml @ 0:268ab1ca4091 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author bgruening
date Mon, 25 Jan 2016 20:21:48 -0500
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-1:000000000000 0:268ab1ca4091
1 <tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
2 <description>plots a histogram of coverage on genomic regions </description>
3 <macros>
4 <token name="@BINARY@">plotCoverage</token>
5 <import>deepTools_macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command>
9 <![CDATA[
10 #set files=[]
11 #set labels=[]
12
13 @multiple_input_bams@
14
15 @BINARY@
16
17 @THREADS@
18
19 --plotFile '$outFileName'
20 --bamfiles '#echo "' '".join($files)#'
21 --labels '#echo "' '".join($labels)#'
22 --plotFileFormat "$outFileFormat"
23
24 #if $outRawCounts:
25 --outRawCounts '$outFileRawCounts'
26 #end if
27
28 #if $advancedOpt.showAdvancedOpt == "yes":
29 --numberOfSamples '$advancedOpt.numberOfSamples'
30 $advancedOpt.skipZeros
31
32 #if str($advancedOpt.region).strip() != '':
33 --region '$advancedOpt.region'
34 #end if
35 --numberOfSamples $advancedOpt.numberOfSamples
36
37 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
38 --plotTitle '$advancedOpt.plotTitle'
39 #end if
40 @ADVANCED_OPTS_READ_PROCESSING@
41 #end if
42
43 ]]>
44 </command>
45 <inputs>
46
47 <expand macro="multiple_input_bams" />
48
49 <conditional name="advancedOpt">
50 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
51 <option value="no" selected="true">no</option>
52 <option value="yes">yes</option>
53 </param>
54 <when value="no" />
55 <when value="yes">
56 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
57 label="Number of samples"
58 help="Number of samples taken from the genome to compute the scaling factors."/>
59 <expand macro="region_limit_operation" />
60 <expand macro="read_processing_options" />
61 <expand macro="skipZeros" />
62 <expand macro="plotTitle" />
63 </when>
64 </conditional>
65
66 <expand macro="input_image_file_format" />
67 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>
68
69
70 </inputs>
71 <outputs>
72 <expand macro="output_image_file_format_not_nested" />
73 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
74 <filter>outRawCounts is True</filter>
75 </data>
76 </outputs>
77 <tests>
78 <test>
79 <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
80 <!--param name="outFileFormat" value="png" /-->
81 <param name="showAdvancedOpt" value="yes" />
82 <param name="plotTitle" value="Test Title from Galaxy" />
83 <param name="outRawCounts" value="True" />
84 <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
85 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="100" />
86 </test>
87 </tests>
88 <help>
89 <![CDATA[
90 **What it does**
91
92 This tools samples 1 million positions in the genome to build
93 a coverage histogram. Multiple bam files are accepted but all should
94 correspond to the same genome assembly.
95
96
97 @REFERENCES@
98 ]]>
99 </help>
100 <expand macro="citations" />
101 </tool>