Mercurial > repos > cpt > cpt_gff_extract_seq
comparison gff3_extract_sequence.xml @ 10:3d9f283ff09d draft default tip
planemo upload commit e14699677f337fd1324aa6898c1388796c5446c1-dirty
| author | cpt |
|---|---|
| date | Fri, 01 Dec 2023 05:01:01 +0000 |
| parents | 759ba1430091 |
| children |
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| 9:9264ac799feb | 10:3d9f283ff09d |
|---|---|
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <command detect_errors="aggressive"><![CDATA[ | 7 <command detect_errors="aggressive"><![CDATA[ |
| 8 @GENOME_SELECTOR_PRE@ | 8 @GENOME_SELECTOR_PRE@ |
| 9 | 9 |
| 10 '$__tool_directory__/gff3_extract_sequence.py' | 10 '$__tool_directory__/gff3_extract_sequence.py' |
| 11 @GENOME_SELECTOR@ | |
| 12 | 11 |
| 13 @INPUT_GFF@ | 12 @GENOME_SELECTOR@ |
| 14 | 13 |
| 15 #if $feature_filter and $feature_filter is not None: | 14 @INPUT_GFF@ |
| 16 --feature_filter '$feature_filter' | 15 |
| 17 #end if | 16 #if $feature_filter and $feature_filter is not None: |
| 18 '$nodesc' | 17 --feature_filter $feature_filter |
| 19 > '$default']]></command> | 18 #end if |
| 19 #if $nodesc | |
| 20 --nodesc | |
| 21 #end if | |
| 22 > '$default']]> | |
| 23 </command> | |
| 20 <inputs> | 24 <inputs> |
| 21 <expand macro="genome_selector"/> | 25 <expand macro="genome_selector"/> |
| 22 <expand macro="gff3_input"/> | 26 <expand macro="gff3_input"/> |
| 23 <param label="Filter for specific feature types" name="feature_filter" type="text" help="Use 'nice_cds' if your features are coming from Apollo, however this will fail on non-Apollo data"/> | 27 <param label="Filter for specific feature types" name="feature_filter" type="text" help="Use 'nice_cds' if your features are coming from Apollo, however this will fail on non-Apollo data"/> |
| 24 <param label="Remove description (use if blasting)" name="nodesc" type="boolean" truevalue="--nodesc" falsevalue=""/> | 28 <param label="Remove description (use if blasting)" name="nodesc" type="boolean" truevalue="--nodesc" falsevalue=""/> |