Mercurial > repos > gaelcge > r_signac_galaxy
comparison signac_createObject.xml @ 0:6e0b320d8b6a draft default tip
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
| author | gaelcge |
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| date | Tue, 02 Aug 2022 19:11:27 +0000 |
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| -1:000000000000 | 0:6e0b320d8b6a |
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| 1 <tool id="signac_createObject" name="CreateObject" version="0.1.0" python_template_version="3.5"> | |
| 2 <description> reads in output files from CellRanger-ATAC and creates a Seurat object containing a ChromatinAssay assay.</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 ln -s $fragment_file fragments.tsv.gz && | |
| 12 ln -s $fragment_index_file fragments.tsv.gz.tbi && | |
| 13 Rscript '${__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 | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param type="data" name="h5_file" label="Select the h5 file containing the filtered peak BC matrix." format="h5" multiple="false" optional="false"/> | |
| 17 <param type="data" name="metadata" label="Select the metadata file." format="csv" multiple="false" optional="false"/> | |
| 18 <param type="select" name="genome" label="Select the respective genome." multiple="false" format="text" optional="false"> | |
| 19 <option value="GRCh38">GRCh38/hg38</option> | |
| 20 <option value="hg19">GRCh37/hg19</option> | |
| 21 <option value="mm10">GRCm38/mm10</option> | |
| 22 </param> | |
| 23 <param type="integer" name="min_cells" value="10" label="Minimum number of cells features needs to be detected in." multiple="false" optional="false"/> | |
| 24 <param type="integer" name="min_features" value="200" label="Minimum number of features for a cell to be retained." multiple="false" optional="false"/> | |
| 25 <param type="data" name="fragment_file" label="Select the fragment file." format="bgzip" multiple="false" optional="false"/> | |
| 26 <param type="data" name="fragment_index_file" label="Select the fragment index file." format="text" multiple="false" optional="false"/> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (CreateObject)"/> | |
| 30 </outputs> | |
| 31 <help><![CDATA[ | |
| 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. | |
| 33 ]]></help> | |
| 34 </tool> |