Mercurial > repos > petr-novak > repeat_annotation_pipeline3

comparison summarize_gff_by_attribute.xml @ 11:5366d5ea04bc draft

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planemo upload commit 9d1b19f98d8b7f0a0d1baf2da63a373d155626f8-dirty
author petr-novak
date Fri, 04 Aug 2023 12:35:32 +0000
parents b53f5a456d01
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10:276efc4cb17f 11:5366d5ea04bc
1 <tool id="summarize_gff_by_attribute" name="Create summary on GFF3 attribute" version="0.1.0" python_template_version="3.5"> 1 <tool id="summarize_gff_by_attribute" name="Create summary on GFF3 attribute" version="0.1.0" python_template_version="3.5">
2 <requirements> 2 <requirements>
3 <requirement type="package">bioconductor-rtracklayer</requirement> 3 <requirement type="package">bioconductor-rtracklayer</requirement>
4 </requirements> 4 </requirements>
5 <required_files>
6 <include type="literal" path="summarize_gff_by_attribute.R"/>
7 </required_files>
5 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
6 $__tool_directory__/summarize_gff_by_attribute.R '$input_gff' $attribute_name '$output_table' 9 Rscript $__tool_directory__/summarize_gff_by_attribute.R '$input_gff' $attribute_name '$output_table'
7 ]]></command> 10 ]]></command>
8 <inputs> 11 <inputs>
9 <param type="data" name="input_gff" format="gff" label="Input GFF"> 12 <param type="data" name="input_gff" format="gff" label="Input GFF">
10 <sanitizer invalid_char=""> 13 <sanitizer invalid_char="">
11 <valid initial="string.ascii_letters,string.digits"> 14 <valid initial="string.ascii_letters,string.digits">
12 <add value="_" /> 15 <add value="_" />
13 </valid> 16 </valid>
14 </sanitizer> 17 </sanitizer>
15 </param> 18 </param>
16 <param type="text" name="attribute_name" label="Name of attribute to summarize"/> 19 <param type="text" name="attribute_name" label="Name of attribute to summarize" optional="false" default="Name"/>
17 </inputs> 20 </inputs>
18 <outputs> 21 <outputs>
19 <data name="output_table" format="tsv" /> 22 <data name="output_table" format="tsv" />
20 </outputs> 23 </outputs>
21 <help><![CDATA[ 24 <help><![CDATA[
22 TODO: Fill in help. 25 Calculate summary statistics on GFF3 attribute. Summary included total number of features and total lenght per attribute value.
23 ]]></help> 26 ]]></help>
24 </tool> 27 </tool>