Mercurial > repos > bgruening > deeptools_plot_coverage

annotate plotCoverage.xml @ 30:ce44b1c88849 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 72ae8f62333aa38d1c63034ddb37184a0f72c64e-dirty
author bgruening
date Fri, 02 Mar 2018 15:30:32 -0500
parents 79032c0e6423
children 1d9d0ef3ab37
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
23
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
1 <tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
29
79032c0e6423 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 25
diff changeset
2 <description>assesses the sequencing depth of BAM/CRAM files </description>
23
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
3 <macros>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
4 <token name="@BINARY@">plotCoverage</token>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
5 <import>deepTools_macros.xml</import>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
6 </macros>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
7 <expand macro="requirements"/>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
8 <command>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
9 <![CDATA[
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
10 #set files=[]
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
11 #set labels=[]
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
12
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
13 @multiple_input_bams@
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
14
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
15 @BINARY@
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
16
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
17 @THREADS@
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
18
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
19 --plotFile '$outFileName'
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
20 --bamfiles #echo " ".join($files)#
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
21 --labels #echo " ".join($labels)#
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
22 --plotFileFormat "$outFileFormat"
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
23
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
24 #if $outRawCounts:
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
25 --outRawCounts '$outFileRawCounts'
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
26 #end if
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
27
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
28 #if $advancedOpt.showAdvancedOpt == "yes":
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
29 --numberOfSamples '$advancedOpt.numberOfSamples'
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
30 $advancedOpt.skipZeros
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
31
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
32 #if str($advancedOpt.region).strip() != '':
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
33 --region '$advancedOpt.region'
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
34 #end if
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
35 --numberOfSamples $advancedOpt.numberOfSamples
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
36
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
37 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
38 --plotTitle '$advancedOpt.plotTitle'
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
39 #end if
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
40 @ADVANCED_OPTS_READ_PROCESSING@
25
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 23
diff changeset
41 @PLOTWIDTHHEIGHT@
23
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
42 @blacklist@
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
43 #end if
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
44
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
45 ]]>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
46 </command>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
47 <inputs>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
48
25
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 23
diff changeset
49 <expand macro="multiple_input_bams" MIN="1"/>
23
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
50
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
51 <conditional name="advancedOpt">
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
52 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
53 <option value="no" selected="true">no</option>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
54 <option value="yes">yes</option>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
55 </param>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
56 <when value="no" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
57 <when value="yes">
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
58 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
59 label="Number of samples"
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
60 help="Number of samples taken from the genome to compute the scaling factors."/>
25
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 23
diff changeset
61 <expand macro="plotWidthHeight" PLOTWIDTH="15.0" PLOTHEIGHT="5.0" />
23
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
62 <expand macro="region_limit_operation" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
63 <expand macro="read_processing_options" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
64 <expand macro="skipZeros" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
65 <expand macro="plotTitle" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
66 <expand macro="blacklist" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
67 </when>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
68 </conditional>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
69
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
70 <expand macro="input_image_file_format" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
71 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
72
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
73
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
74 </inputs>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
75 <outputs>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
76 <expand macro="output_image_file_format_not_nested" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
77 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
78 <filter>outRawCounts is True</filter>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
79 </data>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
80 </outputs>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
81 <tests>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
82 <test>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
83 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
84 <!--param name="outFileFormat" value="png" /-->
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
85 <param name="showAdvancedOpt" value="yes" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
86 <param name="plotTitle" value="Test Title from Galaxy" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
87 <param name="outRawCounts" value="True" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
88 <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
89 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
90 </test>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
91 </tests>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
92 <help>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
93 <![CDATA[
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
94 What it does
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
95 -------------
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
96
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
97 This tool is useful to **assess the sequencing depth** of a given sample.
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
98 It samples 1 million bp, counts the number of overlapping reads and reports
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
99 a coverage histogram that tells you how many bases are covered how many times.
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
100
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
101 **Note:** Multiple BAM files are accepted but all should correspond to the same genome assembly.
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
102
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
103 Output
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
104 ---------
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
105
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
106 The default output is a **panel of two plots** (see below for an example): One is a density plot visualizing the frequencies of read coverages, the other one lets you estimate what fraction of the genome has a depth of sequencing of, for example, 2 overlapping reads or more.
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
107
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
108 The optional output is a table where each row represents the number of reads overlapping with a sampled bp.
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
109
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
110 .. image:: $PATH_TO_IMAGES/plotCoverage_output.png
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
111 :width: 600
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
112 :height: 345
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
113
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
114 Example plot
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
115 -----------------
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
116
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
117 .. image:: $PATH_TO_IMAGES/plotCoverage_annotated.png
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
118 :width: 600
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
119 :height: 291
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
120
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
121
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
122 @REFERENCES@
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
123 ]]>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
124 </help>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
125 <expand macro="citations" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
126 </tool>