Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac_createAssayObject.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_createAssayObject" name="Create Assay Object" version="0.1.0" python_template_version="3.5">
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2 <description> Create Assay Object and Normalize 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-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
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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="data" name="counts" label="Counts Matrix (Output of Gene Activity)" format="rdata" multiple="false" optional="true"/>
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16 <param type="text" name="name" label="Assay Name." multiple="false" optional="true" value="RNA"/>
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17 <param type="integer" name="min_cells" label="Min Cells." multiple="false" optional="false" value="0"/>
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18 <param type="integer" name="min_features" label="Min Features." multiple="false" optional="false" value="0"/>
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19 <param type="select" name="method" label="Method for normalization." value="LogNormalize">
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20 <option value="LogNormalize">LogNormalize</option>
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21 <option value="CLR">CLR</option>
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22 <option value="RC">RC</option>
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23 </param>
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24 <param type="float" name="scale_factor" value='10000' label="Sets the scale factor for cell-level normalization."/>
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25 <param type="select" name="margin" label="If performing CLR normalization, normalize across features (1) or cells (2)." value="1">
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26 <option value="1">1</option>
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27 <option value="2">2</option>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (Create Assay Object - Normalized)"/>
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32 </outputs>
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33 <help><![CDATA[
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34 This tool creates a new assay and runs the NormalizeData function.
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35 ]]></help>
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36 </tool>