Mercurial > repos > gaelcge > r_signac_galaxy
comparison signac_createAssayObject.xml @ 0:6e0b320d8b6a draft default tip
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
| author | gaelcge |
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| date | Tue, 02 Aug 2022 19:11:27 +0000 |
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| -1:000000000000 | 0:6e0b320d8b6a |
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| 1 <tool id="signac_createAssayObject" name="Create Assay Object" version="0.1.0" python_template_version="3.5"> | |
| 2 <description> Create Assay Object and Normalize Data</description> | |
| 3 <macros> | |
| 4 <import>signac_macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <stdio> | |
| 8 <exit_code range="1:" /> | |
| 9 </stdio> | |
| 10 <command><![CDATA[ | |
| 11 Rscript '${__tool_directory__}'/signac-createAssayObject.R --signac-object $signac_object --counts $counts --name $name --min-cells $min_cells --min-features $min_features --method $method --scale-factor $scale_factor --margin $margin --output-object-file $rds_signac_seurat_file | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/> | |
| 15 <param type="data" name="counts" label="Counts Matrix (Output of Gene Activity)" format="rdata" multiple="false" optional="true"/> | |
| 16 <param type="text" name="name" label="Assay Name." multiple="false" optional="true" value="RNA"/> | |
| 17 <param type="integer" name="min_cells" label="Min Cells." multiple="false" optional="false" value="0"/> | |
| 18 <param type="integer" name="min_features" label="Min Features." multiple="false" optional="false" value="0"/> | |
| 19 <param type="select" name="method" label="Method for normalization." value="LogNormalize"> | |
| 20 <option value="LogNormalize">LogNormalize</option> | |
| 21 <option value="CLR">CLR</option> | |
| 22 <option value="RC">RC</option> | |
| 23 </param> | |
| 24 <param type="float" name="scale_factor" value='10000' label="Sets the scale factor for cell-level normalization."/> | |
| 25 <param type="select" name="margin" label="If performing CLR normalization, normalize across features (1) or cells (2)." value="1"> | |
| 26 <option value="1">1</option> | |
| 27 <option value="2">2</option> | |
| 28 </param> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (Create Assay Object - Normalized)"/> | |
| 32 </outputs> | |
| 33 <help><![CDATA[ | |
| 34 This tool creates a new assay and runs the NormalizeData function. | |
| 35 ]]></help> | |
| 36 </tool> |