Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac_geneactivity.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_geneactivity" name="Gene Activity" version="0.1.0" python_template_version="3.5">
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2 <description>Create gene activity matrix</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 ln -s $fragment_file fragments.tsv.gz &&
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12 ln -s $fragment_index_file fragments.tsv.gz.tbi &&
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13 Rscript '${__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
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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="text" name="assay" format="txt" value="NULL" label="Name of assay to use. If blank, use the default assay." multiple="false" optional="true"/>
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20 <param type="data" name="features" label="Features (If NULL, use all features)" format="txt" multiple="false" optional="true"/>
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21 <param type="integer" name="extend_upstream" label="Number of bases to extend upstream of the TSS" multiple="false" optional="false" value="2000"/>
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22 <param type="integer" name="extend_downstream" label="Number of bases to extend downstream of the TSS" multiple="false" optional="false" value="0"/>
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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"/>
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24 <param type="integer" name="max_width" label="Maximum allowed gene width for a gene to be quantified" multiple="false" optional="false" value="500000"/>
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25 </inputs>
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26 <outputs>
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27 <data name="rds_sparse_matrix" format="rdata" label="Sparse Matrix (Gene Activity)"/>
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28 </outputs>
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29 <help><![CDATA[
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30 Compute counts per cell in gene body and promoter region.
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31 ]]></help>
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32 </tool>