Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac_umap.xml @ 0:6e0b320d8b6a draft default tip

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"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
author gaelcge
date Tue, 02 Aug 2022 19:11:27 +0000
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1 <tool id="signac_umap" name="Calculate UMAP" version="0.1.0" python_template_version="3.5">
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2 <description> embedding of scATAC-seq data.</description>
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3 <macros>
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4 <import>signac_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command><![CDATA[
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11 Rscript '${__tool_directory__}'/signac-umap.R --signac-object $signac_object --reduction $reduction_use --dims-use $dims_use --output-object-file $rds_signac_seurat_file
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12 ]]></command>
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13 <inputs>
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14 <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/>
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15 <param type="text" name="reduction_use" value='lsi' label="Dimensional reduction to use for UMAP (default:lsi)." help='Which dimensional reduction (PCA or ICA) to use for the UMAP input.'/>
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16 <param type="text" name="dims_use" value='2,30' label="Dimensional reduction to use for UMAP (default:lsi)." help='How many dimensions to use for UMAP.'/>
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17 </inputs>
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18 <outputs>
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19 <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (UMAP)"/>
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20 </outputs>
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21 <help><![CDATA[
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22 This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object.
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23 ]]></help>
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24 </tool>