Mercurial > repos > petr-novak > repeat_annotation_pipeline3
comparison summarize_gff_by_attribute.xml @ 11:5366d5ea04bc draft
planemo upload commit 9d1b19f98d8b7f0a0d1baf2da63a373d155626f8-dirty
author | petr-novak |
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date | Fri, 04 Aug 2023 12:35:32 +0000 |
parents | b53f5a456d01 |
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10:276efc4cb17f | 11:5366d5ea04bc |
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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"> | 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> |