Mercurial > repos > nilesh > rseqc
diff inner_distance.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/inner_distance.xml Wed Oct 02 02:20:04 2013 -0400 +++ b/inner_distance.xml Mon Oct 07 15:01:13 2013 -0400 @@ -1,57 +1,58 @@ -<tool id="inner_distance" name="Inner Distance" version="1.1"> - <description>calculate the inner distance (or insert size) between two paired RNA reads</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> inner_distance.py -i $input -o output -r $refgene - - #if $bounds.hasLowerBound - -l $bounds.lowerBound - #end if - - #if $bounds2.hasUpperBound - -u $bounds2.upperBound - #end if +<tool id="rseqc_inner_distance" name="Inner Distance" version="1.1"> + <description>calculate the inner distance (or insert size) between two paired RNA reads</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> + inner_distance.py -i $input -o output -r $refgene - #if $steps.step - -s $steps.stepSize - #end if - </command> - <inputs> - <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> - <param name="refgene" type="data" format="bed" label="reference gene model" /> - <conditional name="bounds"> - <param name="hasLowerBound" type="boolean" label="Specify lower bound" value="false"/> - <when value="true"> - <param name="lowerBound" type="integer" value="-250" label="Estimated Lower Bound (bp, default=-250)" /> - </when> - </conditional> - <conditional name="bounds2"> - <param name="hasUpperBound" type="boolean" label="Specify upper bound" value="false" /> - <when value="true"> - <param name="upperBound" type="integer" value="250" label="Estimated Upper Bound (bp, default=250)" /> - </when> - </conditional> - <conditional name="steps"> - <param name="step" type="boolean" label="Specify step size" value="false" /> - <when value="true"> - <param name="stepSize" type="integer" value="5" label="Step size (bp, default=5)" /> - </when> - </conditional> - </inputs> - <outputs> - <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (Text)"/> - <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (Freq Text)" /> - <data format="pdf" name="outputpdf" from_work_dir="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string} (PDF)" /> - <data format="r" name="outputr" from_work_dir="output.inner_distance_plot.r" label="${tool.name} on ${on_string} (R Script)" /> - </outputs> + #if $bounds.hasLowerBound + -l $bounds.lowerBound + #end if + + #if $bounds2.hasUpperBound + -u $bounds2.upperBound + #end if + + #if $steps.step + -s $steps.stepSize + #end if + </command> <stdio> <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> </stdio> - <help> + <inputs> + <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> + <param name="refgene" type="data" format="bed" label="reference gene model" /> + <conditional name="bounds"> + <param name="hasLowerBound" type="boolean" label="Specify lower bound" value="false"/> + <when value="true"> + <param name="lowerBound" type="integer" value="-250" label="Estimated Lower Bound (bp, default=-250)" /> + </when> + </conditional> + <conditional name="bounds2"> + <param name="hasUpperBound" type="boolean" label="Specify upper bound" value="false" /> + <when value="true"> + <param name="upperBound" type="integer" value="250" label="Estimated Upper Bound (bp, default=250)" /> + </when> + </conditional> + <conditional name="steps"> + <param name="step" type="boolean" label="Specify step size" value="false" /> + <when value="true"> + <param name="stepSize" type="integer" value="5" label="Step size (bp, default=5)" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (Text)"/> + <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (Freq Text)" /> + <data format="pdf" name="outputpdf" from_work_dir="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string} (PDF)" /> + <data format="txt" name="outputr" from_work_dir="output.inner_distance_plot.r" label="${tool.name} on ${on_string} (R Script)" /> + </outputs> + <help> inner_distance.py +++++++++++++++++ @@ -71,16 +72,16 @@ ++++++++++++++ Input BAM/SAM file - Alignment file in BAM/SAM format. + Alignment file in BAM/SAM format. Reference gene model - Gene model in BED format. + Gene model in BED format. Estimated Upper/Lower Bounds (defaults=250 and -250) - Estimated upper/lower bounds of inner distance (bp). + Estimated upper/lower bounds of inner distance (bp). Step size (default=5) - Step size of histogram + Step size of histogram Output @@ -118,5 +119,5 @@ .. _RSeQC: http://rseqc.sourceforge.net/ - </help> + </help> </tool>