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planemo upload commit a61591d548f42ff417781e7fe7418dc2901ccc23
author petr-novak
date Tue, 26 Sep 2023 07:28:04 +0000
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1 <tool id="summarize_gff_by_attribute" name="Create summary on GFF3 attribute" version="0.1.0" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package">bioconductor-rtracklayer</requirement>
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4 </requirements>
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5 <required_files>
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6 <include type="literal" path="summarize_gff_by_attribute.R"/>
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7 </required_files>
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript $__tool_directory__/summarize_gff_by_attribute.R '$input_gff' $attribute_name '$output_table'
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10 ]]></command>
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11 <inputs>
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12 <param type="data" name="input_gff" format="gff" label="Input GFF">
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13 <sanitizer invalid_char="">
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14 <valid initial="string.ascii_letters,string.digits">
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15 <add value="_" />
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16 </valid>
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17 </sanitizer>
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18 </param>
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19 <param type="text" name="attribute_name" label="Name of attribute to summarize" optional="false" default="Name"/>
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20 </inputs>
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21 <outputs>
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22 <data name="output_table" format="tsv" />
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23 </outputs>
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24 <help><![CDATA[
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25 Calculate summary statistics on GFF3 attribute. Summary included total number of features and total lenght per attribute value.
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26 ]]></help>
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27 </tool>