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comparison clipping_profile.xml @ 32:580ee0c4bc4e

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Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
author lparsons
date Mon, 07 Oct 2013 15:01:13 -0400
parents cc5eaa9376d8
children
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31:cc5eaa9376d8 32:580ee0c4bc4e
1 <tool id="clipping_profile" name="Clipping Profile" version="1.1"> 1 <tool id="rseqc_clipping_profile" name="Clipping Profile" version="1.1">
2 <description> 2 <description>
3 estimates clipping profile of RNA-seq reads from BAM or SAM file 3 estimates clipping profile of RNA-seq reads from BAM or SAM file
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="2.11.0">R</requirement> 6 <requirement type="package" version="3.0.1">R</requirement>
7 <requirement type="package" version="1.7.1">numpy</requirement> 7 <requirement type="package" version="1.7.1">numpy</requirement>
8 <requirement type="package" version="2.3.7">rseqc</requirement> 8 <requirement type="package" version="2.3.7">rseqc</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command>
11 clipping_profile.py -i $input -o output 11 clipping_profile.py -i $input -o output
12 </command> 12 </command>
13 <inputs>
14 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
15 </inputs>
16 <outputs>
17 <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
18 <data format="r" name="outputr" from_work_dir="output.clipping_profile.r" />
19 </outputs>
20 <stdio> 13 <stdio>
21 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 14 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
22 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 15 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
23 </stdio> 16 </stdio>
24 <help> 17 <inputs>
18 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
19 </inputs>
20 <outputs>
21 <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
22 <data format="txt" name="outputr" from_work_dir="output.clipping_profile.r" />
23 </outputs>
24 <help>
25 clipping_profile.py 25 clipping_profile.py
26 +++++++++++++++++++ 26 +++++++++++++++++++
27 27
28 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file. 28 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
29 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation 29 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
40 ++++++++++++++ 40 ++++++++++++++
41 41
42 .. image:: http://rseqc.sourceforge.net/_images/clipping_good.png 42 .. image:: http://rseqc.sourceforge.net/_images/clipping_good.png
43 :height: 600 px 43 :height: 600 px
44 :width: 600 px 44 :width: 600 px
45 :scale: 80 % 45 :scale: 80 %
46 46
47 ----- 47 -----
48 48
49 About RSeQC 49 About RSeQC
50 +++++++++++ 50 +++++++++++
55 55
56 .. image:: http://rseqc.sourceforge.net/_static/logo.png 56 .. image:: http://rseqc.sourceforge.net/_static/logo.png
57 57
58 .. _RSeQC: http://rseqc.sourceforge.net/ 58 .. _RSeQC: http://rseqc.sourceforge.net/
59 59
60 </help> 60 </help>
61 </tool> 61 </tool>