Mercurial > repos > nilesh > rseqc

annotate clipping_profile.xml @ 40:1e66f05a23aa

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Reupload tarball (all files were again deleted by toolshed).
author lparsons
date Wed, 23 Jul 2014 10:44:50 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
40
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
1 <tool id="rseqc_clipping_profile" name="Clipping Profile" version="2.3.9">
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
2 <description>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
3 estimates clipping profile of RNA-seq reads from BAM or SAM file
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
4 </description>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
5 <requirements>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
6 <requirement type="package" version="3.0.1">R</requirement>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
7 <requirement type="package" version="1.7.1">numpy</requirement>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
8 <requirement type="package" version="2.3.9">rseqc</requirement>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
9 </requirements>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
10 <command>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
11 clipping_profile.py -i $input -o output
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
12 </command>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
13 <stdio>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
14 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
15 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
16 </stdio>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
17 <inputs>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
18 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
19 </inputs>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
20 <outputs>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
21 <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
22 <data format="txt" name="outputr" from_work_dir="output.clipping_profile.r" />
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
23 </outputs>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
24 <help>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
25 clipping_profile.py
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
26 +++++++++++++++++++
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
27
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
28 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
29 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
30 (This means your reads aligner should support clipped mapping).
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
31
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
32 Inputs
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
33 ++++++++++++++
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
34
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
35 Input BAM/SAM file
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
36 Alignment file in BAM/SAM format.
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
37
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
38
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
39 Sample Output
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
40 ++++++++++++++
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
41
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
42 .. image:: http://rseqc.sourceforge.net/_images/clipping_good.png
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
43 :height: 600 px
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
44 :width: 600 px
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
45 :scale: 80 %
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
46
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
47 -----
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
48
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
49 About RSeQC
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
50 +++++++++++
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
51
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
52 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.
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
53
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
54 The RSeQC package is licensed under the GNU GPL v3 license.
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
55
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
56 .. image:: http://rseqc.sourceforge.net/_static/logo.png
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
57
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
58 .. _RSeQC: http://rseqc.sourceforge.net/
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
59
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
60 </help>
1e66f05a23aa Reupload tarball (all files were again deleted by toolshed).
lparsons
parents:
diff changeset
61 </tool>