Mercurial > repos > nilesh > rseqc

comparison geneBody_coverage.xml @ 45:eb339c5849bb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Reupload, toolshed removed all files of previous version.
author lparsons
date Fri, 26 Sep 2014 15:04:18 -0400
parents
children 68ada7ca4cc4
comparison
equal deleted inserted replaced
44:20e0b2dd7882 45:eb339c5849bb
1 <tool 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 $fname = "dataset_1_" + str($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 $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $input.display_name)
19 #set $fname = 'dataset_' + str($index) + '_' + str($safename) + ".bam"
20 ln -s '$additional_input.file' '${fname}' &amp;&amp;
21 ln -s '$additional_input.file.metadata.bam_index' '${fname}.bai' &amp;&amp;
22 echo '${fname}' >> input_list.txt &amp;&amp;
23 #end for
24 geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output
25 </command>
26 <stdio>
27 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
28 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
29 </stdio>
30 <inputs>
31 <param name="input" type="data" label="Additional input .bam files" format="bam" />
32 <repeat name="additionalinputs" title="Input .bam file">
33 <param name="file" type="data" label="Input .bam file" format="bam" />
34 </repeat>
35 <param name="refgene" type="data" label="Reference Genome" format="bed" />
36 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length" help="Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100)." />
37 </inputs>
38 <outputs>
39 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves PDF)" />
40 <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap PDF)">
41 <filter>len(additionalinputs) >= 2</filter>
42 </data>
43 <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage.r" label="${tool.name} on ${on_string} (R Script)" />
44 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
45 </outputs>
46 <help>
47 geneBody_coverage.py
48 ++++++++++++++++++++
49
50 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.
51
52 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.
53
54 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.
55 Coverage skewness was measured by `Pearson’s skewness coefficients &lt;http://en.wikipedia.org/wiki/Skewness#Pearson.27s_skewness_coefficients>`_
56
57 Inputs
58 ++++++++++++++
59
60 Input BAM/SAM file
61 Alignment file in BAM/SAM format.
62
63 Reference gene model
64 Gene Model in BED format.
65
66 Minimum mRNA length
67 Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100).
68
69 Outputs
70 ++++++++++++++
71 Text
72 Table that includes the data used to generate the plots
73
74 R Script
75 R script file that reads the data and generates the plot
76
77 PDF
78 The final plot, in PDF format
79
80 Example plots:
81 .. image:: http://rseqc.sourceforge.net/_images/Aug_26.geneBodyCoverage.curves.png
82 :height: 600 px
83 :width: 600 px
84 :scale: 80 %
85
86 .. image:: http://rseqc.sourceforge.net/_images/Aug_26.geneBodyCoverage.heatMap.png
87 :height: 600 px
88 :width: 600 px
89 :scale: 80 %
90
91 -----
92
93 About RSeQC
94 +++++++++++
95
96 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.
97
98 The RSeQC package is licensed under the GNU GPL v3 license.
99
100 .. image:: http://rseqc.sourceforge.net/_static/logo.png
101
102 .. _RSeQC: http://rseqc.sourceforge.net/
103
104
105
106 </help>
107 </tool>