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author bgruening
date Tue, 10 Feb 2015 03:21:34 -0500
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1 <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="@WRAPPER_VERSION@.0">
2 <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros>
6 <token name="@BINARY@">bamFingerprint</token>
7 <import>deepTools_macros.xml</import>
8 </macros>
9 <command>
10 <![CDATA[
11 @multiple_input_bams@
12
13 bamFingerprint
14
15 @THREADS@
16
17 --bamfiles #echo " ".join($files)
18 --labels #echo " ".join($labels)
19
20 --fragmentLength $fragmentLength
21
22 #set newoutFileName=str($outFileName)+".png"
23 --plotFile $newoutFileName
24
25 #if $output.showOutputSettings == "yes"
26 --plotFileFormat $output.outFileFormat
27 #if $output.saveRawCounts:
28 --outRawCounts '$outFileRawCounts'
29 #end if
30 #else
31 --plotFileFormat 'png'
32 #end if
33
34 #if str($region).strip() != '':
35 --region '$region'
36 #end if
37
38 #if $advancedOpt.showAdvancedOpt == "yes":
39 --binSize '$advancedOpt.binSize'
40 --numberOfSamples '$advancedOpt.numberOfSamples'
41
42 $advancedOpt.doNotExtendPairedEnds
43 $advancedOpt.ignoreDuplicates
44 $advancedOpt.skipZeros
45
46 #if $advancedOpt.minMappingQuality:
47 --minMappingQuality '$advancedOpt.minMappingQuality'
48 #end if
49 #end if
50 ; mv $newoutFileName $outFileName
51 ; rm $temp_dir -rf
52 ]]>
53 </command>
54
55 <inputs>
56 <expand macro="multiple_input_bams" />
57 <expand macro="fragmentLength" />
58 <expand macro="region_limit_operation" />
59
60 <conditional name="advancedOpt">
61 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
62 <option value="no" selected="true">no</option>
63 <option value="yes">yes</option>
64 </param>
65 <when value="no" />
66 <when value="yes">
67 <param name="binSize" type="integer" value="500" min="1"
68 label="Bin size in bp"
69 help="Length in base pairs for a window used to sample the genome."/>
70 <param name="numberOfSamples" type="integer" value="100000" min="1"
71 label="Number of samples"
72 help="Number of samples taken from the genome to compute the scaling factors. (--numberOfSamples)"/>
73 <expand macro="doNotExtendPairedEnds" />
74 <expand macro="ignoreDuplicates" />
75 <expand macro="minMappingQuality" />
76 <expand macro="skipZeros" />
77
78 </when>
79 </conditional>
80 <conditional name="output">
81 <param name="showOutputSettings" type="select" label="Show advanced output settings">
82 <option value="no" selected="true">no</option>
83 <option value="yes">yes</option>
84 </param>
85 <when value="no" />
86 <when value="yes">
87 <expand macro="input_image_file_format" />
88 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
89 </when>
90 </conditional>
91 </inputs>
92 <outputs>
93 <expand macro="output_image_file_format" />
94 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
95 <filter>
96 ((
97 output['showOutputSettings'] == 'yes' and
98 output['saveRawCounts'] is True
99 ))
100 </filter>
101 </data>
102 </outputs>
103 <tests>
104 <test>
105 <repeat name="input_files">
106 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
107 </repeat>
108 <repeat name="input_files">
109 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
110 </repeat>
111 <param name="fragmentLength" value="200" />
112 <param name="showAdvancedOpt" value="no" />
113 <param name="showOutputSettings" value="no" />
114 <output name="outFileName" file="bamFingerprint_result1.png" ftype="png" />
115 </test>
116 </tests>
117 <help>
118 <![CDATA[
119 **What it does**
120
121 This tool is useful to assess the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background signal)
122 and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
123
124 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length.
125 These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
126 and the cumulative sum of read counts are plotted. An ideal input (control sample) with perfect uniform distribution of reads
127 along the genome (i.e. without enrichments in open chromatin etc.) should
128 generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep
129 rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in
130 few bins which corresponds to high, narrow enrichments seen for transcription factors.
131
132
133 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
134
135
136 You can find more details on the bamFingerprint wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint
137
138
139 **Output files**:
140
141 - Diagnostic plot
142 - Data matrix of raw counts
143
144 -----
145
146 @REFERENCES@
147 ]]>
148 </help>
149 <expand macro="citations" />
150 </tool>