Mercurial > repos > nilesh > rseqc
diff clipping_profile.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/clipping_profile.xml Wed Oct 02 02:20:04 2013 -0400 +++ b/clipping_profile.xml Mon Oct 07 15:01:13 2013 -0400 @@ -1,27 +1,27 @@ -<tool id="clipping_profile" name="Clipping Profile" version="1.1"> - <description> - estimates clipping profile of RNA-seq reads from BAM or SAM file - </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> - clipping_profile.py -i $input -o output - </command> - <inputs> - <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" /> - </inputs> - <outputs> - <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" /> - <data format="r" name="outputr" from_work_dir="output.clipping_profile.r" /> - </outputs> +<tool id="rseqc_clipping_profile" name="Clipping Profile" version="1.1"> + <description> + estimates clipping profile of RNA-seq reads from BAM or SAM file + </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> + clipping_profile.py -i $input -o output + </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" label="Input .bam/.sam File" format="bam,sam" /> + </inputs> + <outputs> + <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" /> + <data format="txt" name="outputr" from_work_dir="output.clipping_profile.r" /> + </outputs> + <help> clipping_profile.py +++++++++++++++++++ @@ -42,7 +42,7 @@ .. image:: http://rseqc.sourceforge.net/_images/clipping_good.png :height: 600 px :width: 600 px - :scale: 80 % + :scale: 80 % ----- @@ -57,5 +57,5 @@ .. _RSeQC: http://rseqc.sourceforge.net/ - </help> + </help> </tool>