Mercurial > repos > gaelcge > r_signac_galaxy
comparison signac_geneactivity.xml @ 0:6e0b320d8b6a draft default tip
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
| author | gaelcge |
|---|---|
| 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_geneactivity" name="Gene Activity" version="0.1.0" python_template_version="3.5"> | |
| 2 <description>Create gene activity matrix</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-geneactivity.R --signac-object $signac_object --fragment-file fragments.tsv.gz --assay $assay --features $features --extend-upstream $extend_upstream --extend-downstream $extend_downstream --biotypes $biotypes --max-width $max_width --output-object-file $rds_sparse_matrix | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/> | |
| 17 <param type="data" name="fragment_file" label="Select the fragment file." format="bgzip" multiple="false" optional="false"/> | |
| 18 <param type="data" name="fragment_index_file" label="Select the fragment index file." format="text" multiple="false" optional="false"/> | |
| 19 <param type="text" name="assay" format="txt" value="NULL" label="Name of assay to use. If blank, use the default assay." multiple="false" optional="true"/> | |
| 20 <param type="data" name="features" label="Features (If NULL, use all features)" format="txt" multiple="false" optional="true"/> | |
| 21 <param type="integer" name="extend_upstream" label="Number of bases to extend upstream of the TSS" multiple="false" optional="false" value="2000"/> | |
| 22 <param type="integer" name="extend_downstream" label="Number of bases to extend downstream of the TSS" multiple="false" optional="false" value="0"/> | |
| 23 <param type="text" name="biotypes" label="Gene biotypes to include. If NULL, use all biotypes in the gene annotation" multiple="false" optional="false" value="protein_coding"/> | |
| 24 <param type="integer" name="max_width" label="Maximum allowed gene width for a gene to be quantified" multiple="false" optional="false" value="500000"/> | |
| 25 </inputs> | |
| 26 <outputs> | |
| 27 <data name="rds_sparse_matrix" format="rdata" label="Sparse Matrix (Gene Activity)"/> | |
| 28 </outputs> | |
| 29 <help><![CDATA[ | |
| 30 Compute counts per cell in gene body and promoter region. | |
| 31 ]]></help> | |
| 32 </tool> |