| Previous changeset 1:78407487f758 (2021-11-18) Next changeset 3:14f588312c56 (2021-11-25) |
|
Commit message:
"planemo upload commit 9cbeba115a6e13dd4c007065b7d77dcb400f72fb" |
|
modified:
funannotate_annotate.xml |
| b |
| diff -r 78407487f758 -r aa19eaac7d4b funannotate_annotate.xml --- a/funannotate_annotate.xml Thu Nov 18 21:57:19 2021 +0000 +++ b/funannotate_annotate.xml Thu Nov 25 09:43:01 2021 +0000 |
| [ |
| @@ -8,14 +8,6 @@ </requirements> <version_command>funannotate check --show-versions</version_command> <command><![CDATA[ - -#if $uglyTestingHack == "true": - ## funannotate_db contains some hard coded path, need to rewrite one for tests (not in real life when using data manager) - ## Need to copy too as the test_data is read only on CI - cp -r '${database.fields.path}' './hacked_database' && - sed -i.bak 's|/tmp/prout|'`pwd`'/hacked_database|' './hacked_database/trained_species/fly/info.json' && -#end if - funannotate annotate #if $input.input_type == 'gbk' @@ -28,11 +20,7 @@ --out output -#if $uglyTestingHack == "true": - --database `pwd`'/hacked_database' -#else - --database '$database.fields.path' -#end if +--database '$database.fields.path' #if $sbt: --sbt '${sbt}' @@ -122,7 +110,7 @@ </options> </param> - <param argument="--sbt" type="data" format="sbt" optional="true" label="NCBI submission template file" help="Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)" /> + <param argument="--sbt" type="data" format="txt" optional="true" label="NCBI submission template file" help="Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)" /> <param argument="--eggnog" type="data" format="tabular" optional="true" label="Eggnog-mapper annotations file" help="'annotations' output from 'eggNOG Mapper' tool" /> <param argument="--antismash" type="data" format="genbank" optional="true" label="antiSMASH secondary metabolism results" help="Genbank output from 'Antismash' tool" /> @@ -160,9 +148,6 @@ <option value="need_curating">TSV file of Gene Name/Product defines that need to be curated</option> <option value="new_names_passed">TSV file of Gene Name/Product deflines that passed tbl2asn but are not in Gene2Products database.</option> </param> - - <!-- Need this to change path in the test funannotate_db --> - <param type="hidden" name="uglyTestingHack" value="" /> </inputs> <outputs> <data name='gbk' format='genbank' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="out.gbk"> |