Mercurial > repos > bgruening > deeptools_plot_coverage

annotate plotCoverage.xml @ 38:9f2108594465 draft default tip

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 810c1359b884661d3f5c7372be0f0f88c859a3b9
author bgruening
date Thu, 01 Jun 2023 09:51:11 +0000
parents 18ef8e2c9763
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
38
9f2108594465 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
bgruening
parents: 37
diff changeset
1 <tool id="deeptools_plot_coverage" name="plotCoverage" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
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($labels)#
31
1d9d0ef3ab37 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
bgruening
parents: 29
diff changeset
22 --plotFileFormat '$outFileFormat'
23
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
36
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
28 #if ' '.join(map(str, $BED)) != 'None':
37
18ef8e2c9763 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit ac42d29c298c026aa0c53c9db2553087ebc86b97"
bgruening
parents: 36
diff changeset
29 #set bedFileList=[]
36
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
30 #for $f in $BED:
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
31 #silent $bedFileList.append("'%s'" % $f)
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
32 #end for
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
33 #if $bedFileList != ["'None'"]:
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
34 --BED #echo ' '.join($bedFileList)#
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
35 #end if
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
36 #end if
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
37
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
38 #if $coverageOpt.showCoverageOpt == "yes":
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
39 --outCoverageMetrics '$outFileCoverageMetrics'
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
40 #for $t in $coverageOpt.thresholds:
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
41 -ct $t.coverageThreshold
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
42 #end for
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
43 #end if
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
44
23
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
45 #if $advancedOpt.showAdvancedOpt == "yes":
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
46 --numberOfSamples '$advancedOpt.numberOfSamples'
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
47 $advancedOpt.skipZeros
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
48
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
49 #if str($advancedOpt.region).strip() != '':
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
50 --region '$advancedOpt.region'
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
51 #end if
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
52 --numberOfSamples $advancedOpt.numberOfSamples
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
53
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
54 #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
55 --plotTitle '$advancedOpt.plotTitle'
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
56 #end if
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
57 @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
58 @PLOTWIDTHHEIGHT@
23
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
59 @blacklist@
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
60 #end if
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
61
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
62 ]]>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
63 </command>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
64 <inputs>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
65
25
bed83fb37252 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 23
diff changeset
66 <expand macro="multiple_input_bams" MIN="1"/>
33
f0511595bbd3 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
bgruening
parents: 32
diff changeset
67 <expand macro="custom_sample_labels" />
36
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
68 <param argument="--BED" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
69 label="Regions of interest"
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
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." />
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
71
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
72 <conditional name="coverageOpt">
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
73 <param name="showCoverageOpt" type="select" label="Show coverage metrics options">
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
74 <option value="no" selected="true">No</option>
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
75 <option value="yes">Yes</option>
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
76 </param>
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
77 <when value="no" />
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
78 <when value="yes">
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
79 <param argument="--outCoverageMetrics" type="boolean" label="Save per-threshold coverage metrics?"/>
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
80 <repeat name="thresholds" title="Coverage Thresholds">
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
81 <param argument="--coverageThreshold" type="integer" min="0" label="Coverage Threshold" value="0"/>
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
82 </repeat>
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
83 </when>
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
84 </conditional>
23
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
85
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
86 <conditional name="advancedOpt">
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
87 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
36
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
88 <option value="no" selected="true">No</option>
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
89 <option value="yes">Yes</option>
23
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
90 </param>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
91 <when value="no" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
92 <when value="yes">
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
93 <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
94 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
95 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
96 <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
97 <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
98 <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
99 <expand macro="skipZeros" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
100 <expand macro="plotTitle" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
101 <expand macro="blacklist" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
102 </when>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
103 </conditional>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
104 <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
105 <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
106 </inputs>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
107 <outputs>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
108 <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
109 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
110 <filter>outRawCounts is True</filter>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
111 </data>
36
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
112 <data format="tabular" name="outFileCoverageMetrics" label="${tool.name} on ${on_string}: Threshold Metrics">
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
113 <filter>coverageOpt.outCoverageMetrics is True</filter>
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
114 </data>
23
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
115 </outputs>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
116 <tests>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
117 <test>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
118 <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
119 <!--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
120 <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
121 <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
122 <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
123 <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
124 <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
125 </test>
36
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
126 <test>
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
127 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
128 <param name="showAdvancedOpt" value="yes" />
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
129 <param name="plotTitle" value="Test Title from Galaxy" />
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
130 <param name="showCoverageOpt" value="yes" />
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
131 <param name="coverageThreshold" value="0" />
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
132 <param name="coverageThreshold" value="5" />
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
133 <param name="coverageThreshold" value="10" />
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
134 <param name="coverageThreshold" value="20" />
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
135 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
136 <output name="outFileCoverageMetrics" file="plotCoverage.metrics" ftype="tabular" />
2c17ceeae363 "planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
bgruening
parents: 33
diff changeset
137 </test>
23
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
138 </tests>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
139 <help>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
140 <![CDATA[
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
141 What it does
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
142 -------------
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
143
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
144 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
145 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
146 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
147
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
148 **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
149
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
150 Output
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
151 ---------
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
152
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
153 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
154
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
155 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
156
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
157 .. 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
158 :width: 600
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
159 :height: 345
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
160
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
161 Example plot
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
162 -----------------
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
163
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
164 .. 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
165 :width: 600
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
166 :height: 291
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
167
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
168
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
169 @REFERENCES@
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
170 ]]>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
171 </help>
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
172 <expand macro="citations" />
5f1ab4c4f459 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
bgruening
parents: 17
diff changeset
173 </tool>