comparison signac_find_neighbours.xml @ 0:6e0b320d8b6a draft default tip

"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
author gaelcge
date Tue, 02 Aug 2022 19:11:27 +0000
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1 <tool id="signac_find_neighbours" name="Find neighbours" version="0.1.0" python_template_version="3.5">
2 <description>using the k-nearest neighbour algorithm.</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-find_neighbours.R --signac-object $signac_object --reduction $reduction_use --dims-use $dims_use --output-object-file $rds_signac_seurat_file
12 ]]></command>
13 <inputs>
14 <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/>
15 <param type="text" name="reduction_use" value='lsi' label="Dimensional reduction to use for Find neighbours (default:lsi)." help='Which dimensional reduction (PCA or ICA) to use for the Find neighbours input.'/>
16 <param type="text" name="dims_use" value='2,30' label="Dimensional reduction to use for Find neighbours (default:lsi)." help='How many dimensions to use for Find neighbours.'/>
17 </inputs>
18 <outputs>
19 <data name="rds_signac_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Signac RDS"/>
20 </outputs>
21 <help><![CDATA[
22 This tool runs the Find neighbours function in the Signac pipeline.
23 ]]></help>
24 </tool>