Mercurial > repos > lecorguille > camera_annotate
comparison abims_CAMERA_annotateDiffreport.xml @ 3:729991209550 draft
Uploaded
| author | mmonsoor |
|---|---|
| date | Tue, 15 Sep 2015 05:26:19 -0400 |
| parents | e0afb8854cc4 |
| children | d1c09fc628e5 |
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| 2:947793995ea2 | 3:729991209550 |
|---|---|
| 1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.0.1"> | 1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.0"> |
| 2 | 2 |
| 3 <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> | 3 <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> |
| 4 | 4 |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="package" version="3.1.2">R</requirement> | 6 <requirement type="package" version="3.1.2">R</requirement> |
| 12 | 12 |
| 13 <stdio> | 13 <stdio> |
| 14 <exit_code range="1:" level="fatal" /> | 14 <exit_code range="1:" level="fatal" /> |
| 15 </stdio> | 15 </stdio> |
| 16 | 16 |
| 17 <command> | 17 <command interpreter="Rscript"> |
| 18 CAMERA.r | 18 CAMERA.r |
| 19 xfunction annotatediff image $image | 19 xfunction annotatediff image $image |
| 20 convert_param $convert_param num_digits $num_digits nSlaves \${GALAXY_SLOTS:-1} | 20 convert_param $convert_param num_digits $num_digits nSlaves \${GALAXY_SLOTS:-1} |
| 21 sigma $sigma perfwhm $perfwhm | 21 sigma $sigma perfwhm $perfwhm |
| 22 maxcharge $maxcharge maxiso $maxiso minfrac $minfrac | 22 maxcharge $maxcharge maxiso $maxiso minfrac $minfrac |
| 135 </conditional> | 135 </conditional> |
| 136 | 136 |
| 137 </inputs> | 137 </inputs> |
| 138 | 138 |
| 139 <outputs> | 139 <outputs> |
| 140 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" > | 140 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" /> |
| 141 <discover_datasets pattern="__designation_and_ext__" directory="zip" visible="true" /> | |
| 142 </data> | |
| 143 <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" /> | 141 <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" /> |
| 144 <data name="rdata" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.polarity}.Rdata" > | 142 <data name="rdata" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.polarity}.Rdata" > |
| 145 <change_format> | 143 <change_format> |
| 146 <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" /> | 144 <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" /> |
| 147 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" /> | 145 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" /> |
| 148 </change_format> | 146 </change_format> |
| 149 </data> | 147 </data> |
| 148 <data name="output_zip" format="zip" from_work_dir="Xdiffreport.zip" label="${image.name[:-6]}.annotateDiffreport.zip" > | |
| 149 <filter>(options['option'] == 'show')</filter> | |
| 150 </data> | |
| 150 </outputs> | 151 </outputs> |
| 151 | 152 |
| 152 <tests> | 153 <tests> |
| 153 <test> | 154 <test> |
| 154 <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/> | 155 <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/> |