Mercurial > repos > gaelcge > r_signac_galaxy
comparison signac_subset.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_subset" name="Subset" version="0.1.0" python_template_version="3.5"> | |
| 2 <description> a Signac object based on user defined thresholds.</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 Rscript '${__tool_directory__}'/signac-subset.R --signac-object $signac_object --peak-region-fragments-min $peak_region_fragments_min --peak-region-fragments-max $peak_region_fragments_max --pct-reads-in-peaks $pct_reads_in_peaks --blacklist-ratio $blacklist_ratio --nucleosome-signal $nucleosome_signal --tss-enrichment $tss_enrichment --output-object-file $rds_signac_seurat_file | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/> | |
| 15 <param type="integer" name="peak_region_fragments_min" value='3000' label="Peak region format minimum." help=''/> | |
| 16 <param type="integer" name="peak_region_fragments_max" value='20000' label="Peak region format maximum." help=''/> | |
| 17 <param type="integer" name="pct_reads_in_peaks" value='15' label="Minimum percent of reads in peaks." help=''/> | |
| 18 <param type="float" name="blacklist_ratio" value='0.05' label="Blacklist ratio." help=''/> | |
| 19 <param type="integer" name="nucleosome_signal" value='4' label="Nucleosome signal threshold." help=''/> | |
| 20 <param type="integer" name="tss_enrichment" value='2' label="TSS enrichment signal threshold." help=''/> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data name="rds_signac_seurat_file" format="rdata" label="Signac RDS (subset)"/> | |
| 24 </outputs> | |
| 25 <help><![CDATA[ | |
| 26 This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object. | |
| 27 ]]></help> | |
| 28 </tool> |