Mercurial > repos > petr-novak > repeat_annotation_pipeline3
diff compare_gff.xml @ 11:5366d5ea04bc draft
planemo upload commit 9d1b19f98d8b7f0a0d1baf2da63a373d155626f8-dirty
author | petr-novak |
---|---|
date | Fri, 04 Aug 2023 12:35:32 +0000 |
parents | b53f5a456d01 |
children |
line wrap: on
line diff
--- a/compare_gff.xml Thu May 04 09:27:43 2023 +0000 +++ b/compare_gff.xml Fri Aug 04 12:35:32 2023 +0000 @@ -1,9 +1,13 @@ -<tool id="compare_gff" name="Compare overlap of two GFF3" version="0.1.0" python_template_version="3.5"> +<tool id="compare_gff" name="Compare overlap of two GFF3" version="0.1.0" + python_template_version="3.5"> <requirements> <requirement type="package">bioconductor-rtracklayer</requirement> </requirements> + <required_files> + <include type="literal" path="compare_gff.R"/> + </required_files> <command detect_errors="exit_code"><![CDATA[ - $__tool_directory__/compare_gff.R '$input1_gff' '$input2_gff' '$attribute_name' + Rscript '$__tool_directory__'/compare_gff.R '$input1_gff' '$input2_gff' '$attribute_name' && cp annotation_overlap_long.csv '$out_long' && @@ -11,25 +15,26 @@ ]]></command> <inputs> - <param type="data" name="input1_gff" format="gff" label="First GFF"> - <sanitizer invalid_char=""> - <valid initial="string.ascii_letters,string.digits"> - <add value="_" /> - </valid> - </sanitizer> - </param> - <param type="data" name="input2_gff" format="gff" label="Second GFF"> - <sanitizer invalid_char=""> - <valid initial="string.ascii_letters,string.digits"> - <add value="_" /> - </valid> - </sanitizer> - </param> - <param type="text" name="attribute_name" label="Name of attribute to summarize"/> + <param type="data" name="input1_gff" format="gff" label="First GFF"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits"> + <add value="_"/> + </valid> + </sanitizer> + </param> + <param type="data" name="input2_gff" format="gff" label="Second GFF"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits"> + <add value="_"/> + </valid> + </sanitizer> + </param> + <param type="text" name="attribute_name" label="Name of attribute to summarize" + optional="false" default="Name"/> </inputs> <outputs> <data name="out_long" format="tabular" label="Overlap of annotations - ${input1_gff.hid} and ${input1_gff.hid} (as matrix)" /> + ${input1_gff.hid} and ${input1_gff.hid} (as matrix)"/> <data name="out_wide" format="tabular" label="Overlap of annotations ${input1_gff.hid} and ${input1_gff.hid} (as table)"/> </outputs>