Mercurial > repos > nilesh > rseqc

annotate clipping_profile.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 6b33e31bda10
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
1 <tool id="rseqc_clipping_profile" name="Clipping Profile" version="2.4">
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
2 <description>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
3 estimates clipping profile of RNA-seq reads from BAM or SAM file
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
4 </description>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
5 <requirements>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
6 <requirement type="package" version="3.0.3">R</requirement>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
7 <requirement type="package" version="1.7.1">numpy</requirement>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
8 <requirement type="package" version="2.4">rseqc</requirement>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
9 </requirements>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
10 <command>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
11 clipping_profile.py -i $input -o output
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
12 </command>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
13 <stdio>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
14 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
15 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
16 </stdio>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
17 <inputs>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
18 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
19 </inputs>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
20 <outputs>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
21 <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
22 <data format="txt" name="outputr" from_work_dir="output.clipping_profile.r" />
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
23 </outputs>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
24 <help>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
25 clipping_profile.py
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
26 +++++++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
27
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
28 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
29 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
30 (This means your reads aligner should support clipped mapping).
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
31
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
32 Inputs
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
33 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
34
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
35 Input BAM/SAM file
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
36 Alignment file in BAM/SAM format.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
37
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
38
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
39 Sample Output
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
40 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
41
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
42 .. image:: http://rseqc.sourceforge.net/_images/clipping_good.png
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
43 :height: 600 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
44 :width: 600 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
45 :scale: 80 %
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
46
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
47 -----
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
48
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
49 About RSeQC
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
50 +++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
51
eb339c5849bb Reupload, toolshed removed all files of previous version.
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.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
53
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
54 The RSeQC package is licensed under the GNU GPL v3 license.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
55
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
56 .. image:: http://rseqc.sourceforge.net/_static/logo.png
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
57
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
58 .. _RSeQC: http://rseqc.sourceforge.net/
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
59
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
60 </help>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
61 </tool>