Mercurial > repos > nilesh > rseqc
diff read_duplication.xml @ 32:580ee0c4bc4e
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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--- a/read_duplication.xml Wed Oct 02 02:20:04 2013 -0400 +++ b/read_duplication.xml Mon Oct 07 15:01:13 2013 -0400 @@ -1,27 +1,28 @@ -<tool id="read_duplication" name="Read Duplication" version="1.1"> - <description>determines reads duplication rate with sequence-based and mapping-based strategies</description> - <requirements> - <requirement type="package" version="2.11.0">R</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="2.3.7">rseqc</requirement> - </requirements> - <command> read_duplication.py -i $input -o output -u $upLimit - </command> - <inputs> - <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> - <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" /> - </inputs> - <outputs> - <data format="xls" name="outputxls" from_work_dir="output.dup.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/> - <data format="xls" name="outputseqxls" from_work_dir="output.dup.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/> - <data format="r" name="outputr" from_work_dir="output.DupRate_plot.r" label="${tool.name} on ${on_string} (R Script)" /> - <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" label="${tool.name} on ${on_string} (PDF)" /> - </outputs> +<tool id="rseqc_read_duplication" name="Read Duplication" version="1.1"> + <description>determines reads duplication rate with sequence-based and mapping-based strategies</description> + <requirements> + <requirement type="package" version="3.0.1">R</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="2.3.7">rseqc</requirement> + </requirements> + <command> + read_duplication.py -i $input -o output -u $upLimit + </command> <stdio> <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> </stdio> - <help> + <inputs> + <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> + <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" /> + </inputs> + <outputs> + <data format="xls" name="outputxls" from_work_dir="output.dup.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/> + <data format="xls" name="outputseqxls" from_work_dir="output.dup.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/> + <data format="txt" name="outputr" from_work_dir="output.DupRate_plot.r" label="${tool.name} on ${on_string} (R Script)" /> + <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" label="${tool.name} on ${on_string} (PDF)" /> + </outputs> + <help> read_duplication.py +++++++++++++++++++ @@ -34,10 +35,10 @@ ++++++++++++++ Input BAM/SAM file - Alignment file in BAM/SAM format. + Alignment file in BAM/SAM format. Upper Limit of Plotted Duplicated Times (default=500) - Only used for plotting. + Only used for plotting. Output ++++++++++++++ @@ -66,5 +67,5 @@ .. _RSeQC: http://rseqc.sourceforge.net/ - </help> + </help> </tool>