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abims_CAMERA_annotateDiffreport.xml |
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| diff -r 947793995ea2 -r 729991209550 abims_CAMERA_annotateDiffreport.xml --- a/abims_CAMERA_annotateDiffreport.xml Wed Sep 02 11:32:26 2015 -0400 +++ b/abims_CAMERA_annotateDiffreport.xml Tue Sep 15 05:26:19 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.0.1"> +<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.0"> <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> @@ -14,7 +14,7 @@ <exit_code range="1:" level="fatal" /> </stdio> - <command> + <command interpreter="Rscript"> CAMERA.r xfunction annotatediff image $image convert_param $convert_param num_digits $num_digits nSlaves \${GALAXY_SLOTS:-1} @@ -137,16 +137,17 @@ </inputs> <outputs> - <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" > - <discover_datasets pattern="__designation_and_ext__" directory="zip" visible="true" /> - </data> + <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" /> <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" /> <data name="rdata" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.polarity}.Rdata" > <change_format> <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" /> <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" /> </change_format> - </data> + </data> + <data name="output_zip" format="zip" from_work_dir="Xdiffreport.zip" label="${image.name[:-6]}.annotateDiffreport.zip" > + <filter>(options['option'] == 'show')</filter> + </data> </outputs> <tests> |