Mercurial > repos > gaelcge > r_signac_galaxy
comparison signac_runQC.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_runQC" name="Run quality control" version="0.1.0" python_template_version="3.5"> | |
| 2 <description> on Signac object and plot results.</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 cp $fragment_file fragments.tsv.gz && | |
| 12 cp $fragment_index_file fragments.tsv.gz.tbi && | |
| 13 Rscript '${__tool_directory__}'/signac-runQC.R --signac-object $signac_object --fragment-file fragments.tsv.gz --tss-threshold $tss_threshold --output-object-file $rds_signac_seurat_file --output-tss-plot $output_tss_plot --frag-history-plot $frag_history_plot --png-width $png_width --png-height $png_height | |
| 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="integer" name="tss_threshold" value="2" label=" Transcription start site (TSS) enrichment score threshold for considering cells with a high TSS enrichment for the TSS plot." multiple="false" optional="false"/> | |
| 20 <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.'/> | |
| 21 <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (QC)"/> | |
| 25 <data name="output_tss_plot" format="png" from_work_dir="scATACseq.TSS_plot.png" label="scATACseq.TSS_plot.png"/> | |
| 26 <data name="frag_history_plot" format="png" from_work_dir="scATACseq.fraghist_plot.png" label="scATACseq.fraghist_plot.png"/> | |
| 27 </outputs> | |
| 28 <help><![CDATA[ | |
| 29 This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object. | |
| 30 ]]></help> | |
| 31 </tool> |