Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac_find_clusters.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_find_clusters" name="Identify clusters" version="0.1.0" python_template_version="3.5">
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2 <description>of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm.</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-find_clusters.R --signac-object $signac_object --algorithm $algorithm_use --output-object-file $rds_signac_seurat_file
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12 ]]></command>
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13 <inputs>
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14 <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/>
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15 <param type="integer" name="algorithm_use" value='3' label="Algorithm." help='Algorithm for modularity optimization (1 = original Louvain algorithm; 2 = Louvain algorithm with multilevel refinement; 3 = SLM algorithm; 4 = Leiden algorithm).'/>
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16 </inputs>
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17 <outputs>
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18 <data name="rds_signac_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Signac RDS"/>
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19 </outputs>
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20 <help><![CDATA[
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21 This tool runs the FindClusters step in the Signac workflow.
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22 ]]></help>
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23 </tool>