Mercurial > repos > gaelcge > r_signac_galaxy

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