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comparison read_GC.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
comparison
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31:cc5eaa9376d8 32:580ee0c4bc4e
1 <tool id="read_GC" name="Read GC" version="1.1"> 1 <tool id="rseqc_read_GC" name="Read GC" version="1.1">
2 <description>determines GC% and read count</description> 2 <description>determines GC% and read count</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.11.0">R</requirement> 4 <requirement type="package" version="3.0.1">R</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement> 5 <requirement type="package" version="1.7.1">numpy</requirement>
6 <requirement type="package" version="2.3.7">rseqc</requirement> 6 <requirement type="package" version="2.3.7">rseqc</requirement>
7 </requirements> 7 </requirements>
8 <command> read_GC.py -i $input -o output 8 <command>
9 </command> 9 read_GC.py -i $input -o output
10 <inputs> 10 </command>
11 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
12 </inputs>
13 <outputs>
14 <data format="xls" name="outputxls" from_work_dir="output.GC.xls" label="${tool.name} on ${on_string} (XLS)"/>
15 <data format="r" name="outputr" from_work_dir="output.GC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
16 <data format="pdf" name="outputpdf" from_work_dir="output.GC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
17 </outputs>
18 <stdio> 11 <stdio>
19 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 12 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
20 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 13 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
21 </stdio> 14 </stdio>
22 <help> 15 <inputs>
16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
17 </inputs>
18 <outputs>
19 <data format="xls" name="outputxls" from_work_dir="output.GC.xls" label="${tool.name} on ${on_string} (XLS)"/>
20 <data format="txt" name="outputr" from_work_dir="output.GC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
21 <data format="pdf" name="outputpdf" from_work_dir="output.GC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
22 </outputs>
23 <help>
23 read_GC.py 24 read_GC.py
24 ++++++++++ 25 ++++++++++
25 26
26 27
27 Inputs 28 Inputs
28 ++++++++++++++ 29 ++++++++++++++
29 30
30 Input BAM/SAM file 31 Input BAM/SAM file
31 Alignment file in BAM/SAM format. 32 Alignment file in BAM/SAM format.
32 33
33 Output 34 Output
34 ++++++++++++++ 35 ++++++++++++++
35 36
36 1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count 37 1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count
54 .. image:: http://rseqc.sourceforge.net/_static/logo.png 55 .. image:: http://rseqc.sourceforge.net/_static/logo.png
55 56
56 .. _RSeQC: http://rseqc.sourceforge.net/ 57 .. _RSeQC: http://rseqc.sourceforge.net/
57 58
58 59
59 </help> 60 </help>
60 </tool> 61 </tool>