Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac_runQC.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_runQC" name="Run quality control" version="0.1.0" python_template_version="3.5">
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2 <description> on Signac object and plot results.</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 cp $fragment_file fragments.tsv.gz &&
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12 cp $fragment_index_file fragments.tsv.gz.tbi &&
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13 Rscript '${__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
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14 ]]></command>
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15 <inputs>
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16 <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/>
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17 <param type="data" name="fragment_file" label="Select the fragment file." format="bgzip" multiple="false" optional="false"/>
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18 <param type="data" name="fragment_index_file" label="Select the fragment index file." format="text" multiple="false" optional="false"/>
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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"/>
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20 <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.'/>
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21 <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/>
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22 </inputs>
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23 <outputs>
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24 <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (QC)"/>
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25 <data name="output_tss_plot" format="png" from_work_dir="scATACseq.TSS_plot.png" label="scATACseq.TSS_plot.png"/>
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26 <data name="frag_history_plot" format="png" from_work_dir="scATACseq.fraghist_plot.png" label="scATACseq.fraghist_plot.png"/>
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27 </outputs>
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28 <help><![CDATA[
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29 This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object.
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30 ]]></help>
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31 </tool>