Mercurial > repos > rnateam > ribotaper
changeset 4:74b0ca4446af draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 07674fe3507909d11d7431e3b8c48afcfb1f4b5e"
| author | rnateam |
|---|---|
| date | Tue, 07 Jun 2022 09:19:45 +0000 |
| parents | 579b3be2559f |
| children | 9bc0a9b45b8b |
| files | ribotaper_part1_create_annotation_files.xml test-data/annotation_path/start_stops_FAR_indexed.bed |
| diffstat | 2 files changed, 500 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/ribotaper_part1_create_annotation_files.xml Fri Jun 03 20:17:28 2022 +0000 +++ b/ribotaper_part1_create_annotation_files.xml Tue Jun 07 09:19:45 2022 +0000 @@ -10,12 +10,12 @@ <command><![CDATA[ #if $reference_genome.source == 'history': #set $ref_genome = 'reference.fasta' - ln -s -f '${reference_genome.history_item}' $ref_genome - && samtools faidx $ref_genome + ln -s -f '${reference_genome.history_item}' $ref_genome && + samtools faidx $ref_genome && #else: #set $ref_genome = $reference_genome.index.fields.path #end if - && create_annotations_files.bash + create_annotations_files.bash '${gtf}' '${ref_genome}' $ccdsid @@ -67,6 +67,16 @@ <param name="appris" value="true"/> <output name="output1" file="annotation_path/start_stops_FAR.bed"/> </test> + <test expect_num_outputs="2"> + <param name="gtf" value="test.gtf"/> + <conditional name="reference_genome"> + <param name="source" value="indexed"/> + <param name="index" value="phix174"/> + </conditional> + <param name="ccdsid" value="true"/> + <param name="appris" value="true"/> + <output name="output1" file="annotation_path/start_stops_FAR_indexed.bed"/> + </test> </tests> <help><![CDATA[ Overview
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