comparison geneBody_coverage.xml @ 18:087e32034c95 draft

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author lparsons
date Fri, 26 Sep 2014 10:48:21 -0400
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17:d5edaf8dc974 18:087e32034c95
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id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="2.4">
2 <description>
3 Read coverage over gene body.
4 </description>
5 <requirements>
6 <requirement type="package" version="3.0.3">R</requirement>
7 <requirement type="package" version="1.7.1">numpy</requirement>
8 <requirement type="package" version="2.4">rseqc</requirement>
9 </requirements>
10 <command>
11 #set $safename = ''.join(c in '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $input.display_name)
12 #set $fname = "1_" + str(${safename}) + ".bam"
13 ln -s '${input}' '${fname}' &amp;&amp;
14 ln -s '${input.metadata.bam_index}' '${fname}.bai' &amp;&amp;
15 echo '${fname}' > input_list.txt &amp;&amp;
16 #for $i, $additional_input in enumerate($additionalinputs):
17 #set $index = $i+2
18 #set $fname = ${index}_${input.display_name}.bam
19 ln -s '$additional_input.file' '${fname}' &amp;&amp;
20 ln -s '$additional_input.file.metadata.bam_index' '${fname}.bai' &amp;&amp;
21 echo '${fname}' >> input_list.txt &amp;&amp;
22 #end for
23 geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output
24 </command>
25 <stdio>
26 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
27 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
28 </stdio>
29 <inputs>
30 <param name="input" type="data" label="Additional input .bam files" format="bam" />
31 <repeat name="additionalinputs" title="Input .bam file">
32 <param name="file" type="data" label="Input .bam file" format="bam" />
33 </repeat>
34 <param name="refgene" type="data" label="Reference Genome" format="bed" />
35 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length" help="Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100)." />
36 </inputs>
37 <outputs>
38 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (PDF)" />
39 <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage.r" label="${tool.name} on ${on_string} (R Script)" />
40 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
41 </outputs>
42 <help>
43 geneBody_coverage.py
44 ++++++++++++++++++++
45
46 Read coverage over gene body. This module is used to check if read coverage is uniform and if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates plots illustrating the coverage profile along the gene body.
47
48 If 3 or more BAM files were provided. This program generates a lineGraph and a heatmap. If fewer than 3 BAM files were provided, only lineGraph is generated. See below for examples.
49
50 When heatmap is generated, samples are ranked by the "skewness" of the coverage: Sample with best (worst) coverage will be displayed at the top (bottom) of the heatmap.
51 Coverage skewness was measured by `Pearson’s skewness coefficients &lt;http://en.wikipedia.org/wiki/Skewness#Pearson.27s_skewness_coefficients>`_
52
53 Inputs
54 ++++++++++++++
55
56 Input BAM/SAM file
57 Alignment file in BAM/SAM format.
58
59 Reference gene model
60 Gene Model in BED format.
61
62 Minimum mRNA length
63 Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100).
64
65 Outputs
66 ++++++++++++++
67 Text
68 Table that includes the data used to generate the plots
69
70 R Script
71 R script file that reads the data and generates the plot
72
73 PDF
74 The final plot, in PDF format
75
76 Example plots:
77 .. image:: http://rseqc.sourceforge.net/_images/Aug_26.geneBodyCoverage.curves.png
78 :height: 600 px
79 :width: 600 px
80 :scale: 80 %
81
82 .. image:: http://rseqc.sourceforge.net/_images/Aug_26.geneBodyCoverage.heatMap.png
83 :height: 600 px
84 :width: 600 px
85 :scale: 80 %
86
87 -----
88
89 About RSeQC
90 +++++++++++
91
92 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
93
94 The RSeQC package is licensed under the GNU GPL v3 license.
95
96 .. image:: http://rseqc.sourceforge.net/_static/logo.png
97
98 .. _RSeQC: http://rseqc.sourceforge.net/
99
100
101
102 </help>
103 </tool>