Mercurial > repos > bgruening > deeptools_plot_fingerprint

annotate plotFingerprint.xml @ 22:d92782646040 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e071ca1cc84da473ecc209c9d5e633d90cbc6a78-dirty
author bgruening
date Tue, 11 Jul 2017 04:59:05 -0400
parents d0390db2a666
children 49bf0a3db1d7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
1 <tool id="deeptools_plot_fingerprint" name="plotFingerprint" version="@WRAPPER_VERSION@.0">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
2 <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
3 <macros>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
4 <token name="@BINARY@">plotFingerprint</token>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
5 <import>deepTools_macros.xml</import>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
6 </macros>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
7 <expand macro="requirements" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
8 <command>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
9 <![CDATA[
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
10 @multiple_input_bams@
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
11 @BINARY@
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
12 @THREADS@
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
13 --bamfiles #echo " ".join($files)
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
14 --labels #echo " ".join($labels)
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
15 --plotFile $outFileName
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
16
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
17 #if $output.showOutputSettings == "yes"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
18 --plotFileFormat $output.outFileFormat
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
19 #if $output.saveRawCounts:
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
20 --outRawCounts '$outFileRawCounts'
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
21 #end if
16
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
22 #if $output.saveQualityMetrics:
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
23 --outQualityMetrics '$outFileQualityMetrics'
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
24 #if $output.JSDsample:
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
25 #if "'{}'".format($output.JSDsample.display_name) in $labels:
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
26 #set JSDidx = $labels.index("'{}'".format($output.JSDsample.display_name))
20
d0390db2a666 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 16
diff changeset
27 --JSDsample "${JSDidx}.bam"
16
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
28 #end if
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
29 #end if
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
30 #end if
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
31 #else
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
32 --plotFileFormat 'png'
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
33 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
34
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
35 #if str($region).strip() != '':
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
36 --region '$region'
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
37 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
38
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
39 #if $advancedOpt.showAdvancedOpt == "yes":
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
40 --binSize '$advancedOpt.binSize'
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
41 --numberOfSamples '$advancedOpt.numberOfSamples'
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
42
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
43 $advancedOpt.ignoreDuplicates
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
44 $advancedOpt.skipZeros
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
45
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
46 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
47 --plotTitle '$advancedOpt.plotTitle'
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
48 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
49 @ADVANCED_OPTS_READ_PROCESSING@
12
ea9198c920f6 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296
bgruening
parents: 10
diff changeset
50 @blacklist@
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
51 #end if
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
52 ]]>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
53 </command>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
54
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
55 <inputs>
20
d0390db2a666 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 16
diff changeset
56 <expand macro="multiple_input_bams" MIN="1"/>
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
57 <expand macro="region_limit_operation" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
58
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
59 <conditional name="advancedOpt">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
60 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
61 <option value="no" selected="true">no</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
62 <option value="yes">yes</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
63 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
64 <when value="no" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
65 <when value="yes">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
66 <param argument="--binSize" type="integer" value="500" min="1"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
67 label="Bin size in bases"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
68 help="Length in bases for a window used to sample the genome."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
69 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
70 label="Number of samples"
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
71 help="Number of samples taken from the genome to compute the scaling factors."/>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
72 <expand macro="read_processing_options" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
73 <expand macro="skipZeros" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
74 <expand macro="plotTitle" />
12
ea9198c920f6 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296
bgruening
parents: 10
diff changeset
75 <expand macro="blacklist" />
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
76 </when>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
77 </conditional>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
78
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
79 <conditional name="output">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
80 <param name="showOutputSettings" type="select" label="Show advanced output settings">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
81 <option value="no" selected="true">no</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
82 <option value="yes">yes</option>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
83 </param>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
84 <when value="no" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
85 <when value="yes">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
86 <expand macro="input_image_file_format" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
87 <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
16
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
88 <param name="saveQualityMetrics" type="boolean" label="Save quality metrics"
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
89 help="The file will have one row per input BAM file and columns containing a variety of QC metrics. For the full description of all metrics and their interpretation, please see our online documentation: http://deeptools.readthedocs.io/en/latest/content/feature/plotFingerprint_QC_metrics.html. (--outQualityMetrics)"/>
20
d0390db2a666 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 16
diff changeset
90 <param name="JSDsample" type="data" format="bam" optional="true"
16
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
91 label="Jensen-Shannon distance reference sample"
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
92 help="If output metrics should be saved, then use this sample as the reference for computing the Jensen-Shannon distance and CHANCE metrics of all other samples. Normally this is an input sample. If you don't specify this, then these metrics will not be computed. This is only applicable if quality metrics are being saved. (--JSDsample)" />
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
93 </when>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
94 </conditional>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
95 </inputs>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
96 <outputs>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
97 <expand macro="output_image_file_format" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
98 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
99 <filter>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
100 ((
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
101 output['showOutputSettings'] == 'yes' and
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
102 output['saveRawCounts'] is True
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
103 ))
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
104 </filter>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
105 </data>
16
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
106 <data format="tabular" name="outFileQualityMetrics" label="${tool.name} on ${on_string}: quality metrics">
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
107 <filter>
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
108 ((
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
109 output['showOutputSettings'] == 'yes' and
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
110 output['saveQualityMetrics'] is True
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
111 ))
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
112 </filter>
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
113 </data>
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
114 </outputs>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
115 <tests>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
116 <test>
10
d0a10af43611 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty
bgruening
parents: 7
diff changeset
117 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
118 <param name="showAdvancedOpt" value="no" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
119 <param name="showOutputSettings" value="no" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
120 <output name="outFileName" file="plotFingerprint_result1.png" ftype="png" compare="sim_size" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
121 </test>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
122 <test>
10
d0a10af43611 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty
bgruening
parents: 7
diff changeset
123 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
124 <param name="showAdvancedOpt" value="yes" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
125 <param name="showOutputSettings" value="yes" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
126 <param name="saveRawCounts" value="True" />
16
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
127 <param name="saveQualityMetrics" value="True" />
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
128 <param name="plotTitle" value="Test Fingerprint Plot" />
16
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
129 <param name="JSDsample" value="bowtie2 test1.bam" ftype="bam" />
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
130 <output name="outFileName" file="plotFingerprint_result2.png" ftype="png" compare="sim_size" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
131 <output name="outFileRawCounts" file="plotFingerprint_result2.tabular" ftype="tabular" />
16
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
132 <output name="outFileQualityMetrics" file="plotFingerprint_quality_metrics.tabular" ftype="tabular" />
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
133 </test>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
134 </tests>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
135 <help>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
136 <![CDATA[
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
137
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
138
4
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
139 What it does
7
5c4660838326 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
bgruening
parents: 6
diff changeset
140 ------------
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
141
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
142 This tool is useful for assessing the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background)
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
143 and is based on a method described in Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
144
4
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
145
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
146 Output
7
5c4660838326 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
bgruening
parents: 6
diff changeset
147 ------
4
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
148
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
149 The default output is a diagnostic plot (see below for an example and further down for some background information).
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
150
16
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
151 Optionally, you can obtain the table of raw values that were used to generate the plot.
4
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
152
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
153 .. image:: $PATH_TO_IMAGES/plotFingerprint_output.png
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
154 :width: 600
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
155 :height: 395
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
156
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
157
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
158 Example plot
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
159 -------------
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
160
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
161 What follows is the output of ``plotFingerprint`` with our test ChIP-Seq data sets, limiting the analysis to chromosome X. Single-end reads were extended to
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
162 200 bp (advanced options).
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
163
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
164 .. image:: $PATH_TO_IMAGES/bamFP_galaxy_output.png
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
165 :width: 600
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
166 :height: 450
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
167
7
5c4660838326 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
bgruening
parents: 6
diff changeset
168 -----
4
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
169
6
b9141fe4e00c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 7150f0c106abd56920767518cc331ef6e4e7f439
bgruening
parents: 4
diff changeset
170 Theoretical Background
b9141fe4e00c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 7150f0c106abd56920767518cc331ef6e4e7f439
bgruening
parents: 4
diff changeset
171 ----------------------
4
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
172
16
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
173 The tool first samples indexed BAM files and sums the per-base coverage of reads/fragments overlapping a window (bin) of the specified length.
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
174 These values are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
175 and the cumulative sum plotted. An ideal input (control) with a uniform distribution of reads alignments
2768f00a7d25 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
bgruening
parents: 12
diff changeset
176 and infinite sequencing depth will result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
177 of reads accumulating in just a few bins and the resulting plot showing a steep rise toward the right-most edge. Such results are
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
178 most commonly seen with transcription factors.
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
179
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
180
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
181 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
4
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
182 :width: 600
30481ee59a46 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
bgruening
parents: 0
diff changeset
183 :height: 294
0
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
184
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
185 -----
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
186
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
187 @REFERENCES@
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
188 ]]>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
189 </help>
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
190 <expand macro="citations" />
bb874a0121d5 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b'a4965adc865b4c85b35ed205bc10821edc104f20'
bgruening
parents:
diff changeset
191 </tool>