Mercurial > repos > petr-novak > repeat_annotation_pipeline3
comparison 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 |
comparison
equal
deleted
inserted
replaced
| 10:276efc4cb17f | 11:5366d5ea04bc |
|---|---|
| 1 <tool id="compare_gff" name="Compare overlap of two GFF3" version="0.1.0" python_template_version="3.5"> | 1 <tool id="compare_gff" name="Compare overlap of two GFF3" version="0.1.0" |
| 2 python_template_version="3.5"> | |
| 2 <requirements> | 3 <requirements> |
| 3 <requirement type="package">bioconductor-rtracklayer</requirement> | 4 <requirement type="package">bioconductor-rtracklayer</requirement> |
| 4 </requirements> | 5 </requirements> |
| 6 <required_files> | |
| 7 <include type="literal" path="compare_gff.R"/> | |
| 8 </required_files> | |
| 5 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
| 6 $__tool_directory__/compare_gff.R '$input1_gff' '$input2_gff' '$attribute_name' | 10 Rscript '$__tool_directory__'/compare_gff.R '$input1_gff' '$input2_gff' '$attribute_name' |
| 7 && | 11 && |
| 8 cp annotation_overlap_long.csv '$out_long' | 12 cp annotation_overlap_long.csv '$out_long' |
| 9 && | 13 && |
| 10 cp annotation_overlap.csv '$out_wide' | 14 cp annotation_overlap.csv '$out_wide' |
| 11 | 15 |
| 12 ]]></command> | 16 ]]></command> |
| 13 <inputs> | 17 <inputs> |
| 14 <param type="data" name="input1_gff" format="gff" label="First GFF"> | 18 <param type="data" name="input1_gff" format="gff" label="First GFF"> |
| 15 <sanitizer invalid_char=""> | 19 <sanitizer invalid_char=""> |
| 16 <valid initial="string.ascii_letters,string.digits"> | 20 <valid initial="string.ascii_letters,string.digits"> |
| 17 <add value="_" /> | 21 <add value="_"/> |
| 18 </valid> | 22 </valid> |
| 19 </sanitizer> | 23 </sanitizer> |
| 20 </param> | 24 </param> |
| 21 <param type="data" name="input2_gff" format="gff" label="Second GFF"> | 25 <param type="data" name="input2_gff" format="gff" label="Second GFF"> |
| 22 <sanitizer invalid_char=""> | 26 <sanitizer invalid_char=""> |
| 23 <valid initial="string.ascii_letters,string.digits"> | 27 <valid initial="string.ascii_letters,string.digits"> |
| 24 <add value="_" /> | 28 <add value="_"/> |
| 25 </valid> | 29 </valid> |
| 26 </sanitizer> | 30 </sanitizer> |
| 27 </param> | 31 </param> |
| 28 <param type="text" name="attribute_name" label="Name of attribute to summarize"/> | 32 <param type="text" name="attribute_name" label="Name of attribute to summarize" |
| 33 optional="false" default="Name"/> | |
| 29 </inputs> | 34 </inputs> |
| 30 <outputs> | 35 <outputs> |
| 31 <data name="out_long" format="tabular" label="Overlap of annotations | 36 <data name="out_long" format="tabular" label="Overlap of annotations |
| 32 ${input1_gff.hid} and ${input1_gff.hid} (as matrix)" /> | 37 ${input1_gff.hid} and ${input1_gff.hid} (as matrix)"/> |
| 33 <data name="out_wide" format="tabular" label="Overlap of annotations | 38 <data name="out_wide" format="tabular" label="Overlap of annotations |
| 34 ${input1_gff.hid} and ${input1_gff.hid} (as table)"/> | 39 ${input1_gff.hid} and ${input1_gff.hid} (as table)"/> |
| 35 </outputs> | 40 </outputs> |
| 36 <help><![CDATA[ | 41 <help><![CDATA[ |
| 37 Compare overlaps in two GFF3 by selected attribute. Overlap is reported a number of bases. It expects not overlap within individuals GFF3. | 42 Compare overlaps in two GFF3 by selected attribute. Overlap is reported a number of bases. It expects not overlap within individuals GFF3. |