Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac_LSI.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_lsi" name="Latent semantic indexing (LSI)" version="0.1.0" python_template_version="3.5">
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2 <description> pferofrms normalization and linear dimensional reduction (TF-IDF followed by SVD).</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-LSI.R --signac-object $signac_object --min-cutoff $min_cutoff --png-width $png_width --png-height $png_height --output-depthcor $output_depthcor_plot --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="min_cutoff" value='q0' label="Variable features cutoff to use." help='Cutoff for feature to be included in the VariableFeatures for the object.'/>
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16 <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.'/>
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17 <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/>
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18 </inputs>
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19 <outputs>
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20 <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (LSI)"/>
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21 <data name="output_depthcor_plot" format="png" from_work_dir="Signac.Depthcor_plot.png" label="Signac.Depthcor_plot.png"/>
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22 </outputs>
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23 <help><![CDATA[
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24 This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object.
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25 ]]></help>
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26 </tool>