comparison multiBamSummary.xml @ 0:04b612e24e62 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author bgruening
date Mon, 25 Jan 2016 20:18:00 -0500
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children f2a582e0314d
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-1:000000000000 0:04b612e24e62
1 <tool id="deeptools_multi_bam_summary" name="multiBamSummary" version="@WRAPPER_VERSION@.0">
2 <description>calculates average read coverages for a list of two or more BAM files</description>
3 <macros>
4 <token name="@BINARY@">multiBamSummary</token>
5 <import>deepTools_macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>
9 <![CDATA[
10 #set files=[]
11 #set labels=[]
12
13 @multiple_input_bams@
14 @BINARY@
15 $mode.modeOpt
16 @THREADS@
17
18 --outFileName '$outFile'
19 --bamfiles '#echo "' '".join($files)#'
20 --labels '#echo "' '".join($labels)#'
21
22 #if $outRawCounts:
23 --outRawCounts '$outFileRawCounts'
24 #end if
25
26 #if $mode.modeOpt == "bins":
27 --binSize '$mode.binSize'
28 --distanceBetweenBins '$mode.distanceBetweenBins'
29 #else:
30 --BED $mode.region_file
31 #end if
32
33 #if str($region).strip() != '':
34 --region '$region'
35 #end if
36
37 #if $advancedOpt.showAdvancedOpt == "yes":
38 @ADVANCED_OPTS_READ_PROCESSING@
39 #end if
40 ]]>
41 </command>
42
43 <inputs>
44 <expand macro="multiple_input_bams" />
45
46 <conditional name="mode">
47 <param name="modeOpt" type="select" label="Choose computation mode"
48 help="In the bins mode, the coverage is computed for equally
49 sized bins. In the BED file mode, a list of genomic regions in BED
50 format has to be given. For each region in the BED file the number of
51 overlapping reads is counted in each of the BAM files.
52 ">
53 <option value="bins" selected="true">Bins</option>
54 <option value="BED-file">Limit calculation to certain regions (BED file)</option>
55 </param>
56 <when value="bins">
57 <param name="binSize" type="integer" value="10000" min="1"
58 label="Bin size in bp"
59 help="Length in bases of the window used to sample the genome. (--binSize)"/>
60
61 <expand macro="distanceBetweenBins" />
62
63 </when>
64 <when value="BED-file">
65 <param name="region_file" type="data" format="bed"
66 label="Region file in BED format"
67 help="Coverage is computed for the number of reads that overlap such regions."/>
68 </when>
69 </conditional>
70
71 <expand macro="region_limit_operation" />
72
73 <expand macro="advancedOpt_scaffold">
74 <expand macro="read_processing_options" />
75 </expand>
76
77 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/>
78
79 </inputs>
80 <outputs>
81 <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" />
82 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
83 <filter>outRawCounts is True</filter>
84 </data>
85 </outputs>
86 <tests>
87 <test>
88 <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
89 <param name="modeOpt" value="bins" />
90 <param name="binSize" value="10" />
91 <output name="outFile" file="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
92 </test>
93 <test>
94 <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
95 <param name="modeOpt" value="BED-file" />
96 <param name="region_file" value="multiBamSummary_regions.bed" />
97 <output name="outFile" file="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
98 </test>
99
100
101 </tests>
102 <help>
103 <![CDATA[
104
105 **What it does**
106
107 This tool generates a matrix of read-coverages for a list of genomic regions and at least two samples (BAM files).
108 The genome is split into bins of the given size. For each bin, the number of reads found in it in each BAM file is counted.
109 Alternatively, a bed file with pre-defined genomic regions can be provided. In each case the calculation can further be limited to
110 a given genomic interval (e.g. a given chromosome). This option is mostly used for testing and efficiency.
111 A typical follow-up application is to check and visualize the similarity between replicates or published data sets (see: plotPCA and plotCorrelation).
112
113 **Output files**:
114
115 - **score matrix**: a compressed matrix where every row corresponds to a genomic region (or bin) and each column corresponds to a sample (BAM file)
116 - Optional : Uncompressed **score matrix**, in case you want to analyse the coverage scores yourself. (Select to "Save raw counts" from above)
117
118 =======
119
120 .. image:: $PATH_TO_IMAGES/QC_multiBamSummary_humanSamples.png
121 :alt: Heatmap of RNA Polymerase II ChIP-seq
122
123
124 You can find more details on the multiBamSummary doc page: https://deeptools.readthedocs.org/en/master/content/tools/multiBamSummary.html
125
126 -----
127
128 @REFERENCES@
129 ]]>
130 </help>
131 <expand macro="citations" />
132 </tool>