Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac_createObject.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_createObject" name="CreateObject" version="0.1.0" python_template_version="3.5">
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2 <description> reads in output files from CellRanger-ATAC and creates a Seurat object containing a ChromatinAssay assay.</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 ln -s $fragment_file fragments.tsv.gz &&
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12 ln -s $fragment_index_file fragments.tsv.gz.tbi &&
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13 Rscript '${__tool_directory__}'/signac-createObject.R --h5-file $h5_file --metadata $metadata --genome $genome --fragment-file fragments.tsv.gz --output-object-file $rds_signac_seurat_file --min-cells $min_cells --min-features $min_features
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14 ]]></command>
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15 <inputs>
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16 <param type="data" name="h5_file" label="Select the h5 file containing the filtered peak BC matrix." format="h5" multiple="false" optional="false"/>
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17 <param type="data" name="metadata" label="Select the metadata file." format="csv" multiple="false" optional="false"/>
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18 <param type="select" name="genome" label="Select the respective genome." multiple="false" format="text" optional="false">
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19 <option value="GRCh38">GRCh38/hg38</option>
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20 <option value="hg19">GRCh37/hg19</option>
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21 <option value="mm10">GRCm38/mm10</option>
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22 </param>
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23 <param type="integer" name="min_cells" value="10" label="Minimum number of cells features needs to be detected in." multiple="false" optional="false"/>
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24 <param type="integer" name="min_features" value="200" label="Minimum number of features for a cell to be retained." multiple="false" optional="false"/>
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25 <param type="data" name="fragment_file" label="Select the fragment file." format="bgzip" multiple="false" optional="false"/>
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26 <param type="data" name="fragment_index_file" label="Select the fragment index file." format="text" multiple="false" optional="false"/>
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27 </inputs>
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28 <outputs>
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29 <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (CreateObject)"/>
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30 </outputs>
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31 <help><![CDATA[
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32 This tool runs the first step in the Signac pipeline, which is to read in the filtered peak BC matrix, the metadata and the fragment file and create a Seurat object.
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33 ]]></help>
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34 </tool>