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comparison bam_stat.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="bam_stat" name="BAM/SAM Mapping Stats" version="1.1"> 1 <tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="1.1">
2 <description> 2 <description>
3 reads mapping statistics for a provided BAM or SAM file. 3 reads mapping statistics for a provided BAM or SAM file.
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1.7.1">numpy</requirement> 6 <requirement type="package" version="1.7.1">numpy</requirement>
7 <requirement type="package" version="2.3.7">rseqc</requirement> 7 <requirement type="package" version="2.3.7">rseqc</requirement>
8 </requirements>s 8 </requirements>s
9 <command> 9 <command>
10 bam_stat.py -i $input -q $mapqual 2> $output 10 bam_stat.py -i $input -q $mapqual 2> $output
11 </command> 11 </command>
12 <inputs>
13 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
14 <param label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" />
15 </inputs>
16 <outputs>
17 <data format="txt" name="output" />
18 </outputs>
19 <stdio> 12 <stdio>
20 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 13 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
21 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 14 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
22 </stdio> 15 </stdio>
23 <help> 16 <inputs>
17 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
18 <param label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" />
19 </inputs>
20 <outputs>
21 <data format="txt" name="output" />
22 </outputs>
23 <help>
24 bam_stat.py 24 bam_stat.py
25 +++++++++++ 25 +++++++++++
26 26
27 This program is used to calculate reads mapping statistics from provided BAM 27 This program is used to calculate reads mapping statistics from provided BAM
28 file. This script determines "uniquely mapped reads" from `mapping quality`_, 28 file. This script determines "uniquely mapped reads" from `mapping quality`_,
59 .. image:: http://rseqc.sourceforge.net/_static/logo.png 59 .. image:: http://rseqc.sourceforge.net/_static/logo.png
60 60
61 .. _RSeQC: http://rseqc.sourceforge.net/ 61 .. _RSeQC: http://rseqc.sourceforge.net/
62 .. _`mapping quality`: http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores 62 .. _`mapping quality`: http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores
63 63
64 </help> 64 </help>
65 </tool> 65 </tool>