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comparison plotFingerprint.xml @ 0:c1b46e0cb7ca draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author bgruening
date Mon, 25 Jan 2016 20:15:58 -0500
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1 <tool id="deeptools_plot_fingerprint" name="plotFingerprint" version="@WRAPPER_VERSION@.0">
2 <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
3 <macros>
4 <token name="@BINARY@">plotFingerprint</token>
5 <import>deepTools_macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>
9 <![CDATA[
10 @multiple_input_bams@
11 @BINARY@
12 @THREADS@
13 --bamfiles #echo " ".join($files)
14 --labels #echo " ".join($labels)
15 --plotFile $outFileName
16
17 #if $output.showOutputSettings == "yes"
18 --plotFileFormat $output.outFileFormat
19 #if $output.saveRawCounts:
20 --outRawCounts '$outFileRawCounts'
21 #end if
22 #else
23 --plotFileFormat 'png'
24 #end if
25
26 #if str($region).strip() != '':
27 --region '$region'
28 #end if
29
30 #if $advancedOpt.showAdvancedOpt == "yes":
31 --binSize '$advancedOpt.binSize'
32 --numberOfSamples '$advancedOpt.numberOfSamples'
33
34 $advancedOpt.ignoreDuplicates
35 $advancedOpt.skipZeros
36
37 #if $advancedOpt.minMappingQuality:
38 --minMappingQuality '$advancedOpt.minMappingQuality'
39 #end if
40
41 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
42 --plotTitle '$advancedOpt.plotTitle'
43 #end if
44 @ADVANCED_OPTS_READ_PROCESSING@
45 #end if
46 ]]>
47 </command>
48
49 <inputs>
50 <expand macro="multiple_input_bams" />
51 <expand macro="region_limit_operation" />
52
53 <conditional name="advancedOpt">
54 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
55 <option value="no" selected="true">no</option>
56 <option value="yes">yes</option>
57 </param>
58 <when value="no" />
59 <when value="yes">
60 <param argument="--binSize" type="integer" value="500" min="1"
61 label="Bin size in bases"
62 help="Length in bases for a window used to sample the genome."/>
63 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
64 label="Number of samples"
65 help="Number of samples taken from the genome to compute the scaling factors."/>
66 <expand macro="read_processing_options" />
67 <expand macro="skipZeros" />
68 <expand macro="plotTitle" />
69 </when>
70 </conditional>
71
72 <conditional name="output">
73 <param name="showOutputSettings" type="select" label="Show advanced output settings">
74 <option value="no" selected="true">no</option>
75 <option value="yes">yes</option>
76 </param>
77 <when value="no" />
78 <when value="yes">
79 <expand macro="input_image_file_format" />
80 <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
81 </when>
82 </conditional>
83 </inputs>
84 <outputs>
85 <expand macro="output_image_file_format" />
86 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
87 <filter>
88 ((
89 output['showOutputSettings'] == 'yes' and
90 output['saveRawCounts'] is True
91 ))
92 </filter>
93 </data>
94 </outputs>
95 <tests>
96 <test>
97 <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
98 <param name="showAdvancedOpt" value="no" />
99 <param name="showOutputSettings" value="no" />
100 <output name="outFileName" file="plotFingerprint_result1.png" ftype="png" compare="sim_size" />
101 </test>
102 <test>
103 <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
104 <param name="showAdvancedOpt" value="yes" />
105 <param name="showOutputSettings" value="yes" />
106 <param name="saveRawCounts" value="True" />
107 <param name="plotTitle" value="Test Fingerprint Plot" />
108 <output name="outFileName" file="plotFingerprint_result2.png" ftype="png" compare="sim_size" />
109 <output name="outFileRawCounts" file="plotFingerprint_result2.tabular" ftype="tabular" />
110 </test>
111 </tests>
112 <help>
113 <![CDATA[
114
115
116 **What it does**
117
118 This tool is useful for assessing the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background)
119 and is based on a method described in Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
120
121 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of the specified length.
122 These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
123 and the cumulative sum of read counts are plotted. An ideal input (control) with a uniform distribution of reads alignments
124 result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion
125 of reads accumulating in just a few bins and the resulting plot showing a steep rise toward the right-most edge. Such results are
126 most commonly seen with transcription factors.
127
128
129 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
130
131
132 You can find more details on the plotFingerprint doc page: https://deeptools.readthedocs.org/en/master/content/tools/plotFingerprint.html
133
134
135 **Output files**:
136
137 - Diagnostic plot
138 - (optional) Data matrix of raw counts
139
140 **Output with test dataset**:
141
142 What follows is the output of plotFingerprint with our test ChIP-Seq datasets, limiting analysis to chromosome X. Single-end reads were extended to
143 200 bp (advanced options).
144
145 .. image:: $PATH_TO_IMAGES/bamFP_galaxy_output.png
146
147
148 -----
149
150 @REFERENCES@
151 ]]>
152 </help>
153 <expand macro="citations" />
154 </tool>