Mercurial > repos > nml > biohansel
changeset 7:3360158bb0c5 draft
planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
| author | nml |
|---|---|
| date | Mon, 13 May 2019 09:42:08 -0400 |
| parents | ba6a0af656a6 |
| children | 4fa9d5e748d4 |
| files | biohansel.xml |
| diffstat | 1 files changed, 16 insertions(+), 12 deletions(-) [+] |
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--- a/biohansel.xml Wed Mar 20 13:44:02 2019 -0400 +++ b/biohansel.xml Mon May 13 09:42:08 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="biohansel" name="biohansel" version="2.1.5"> +<tool id="biohansel" name="biohansel" version="2.1.6"> <description>SNP subtyping of genome sequence reads or assemblies</description> <requirements> <requirement type="package" version="2.1.1">bio_hansel</requirement> @@ -72,7 +72,7 @@ #end if ## Checking for custom scheme. -#if $type_of_scheme.scheme_type == "custom": +#if $type_of_scheme.scheme_check == "custom": #if $type_of_scheme.scheme_input.is_of_type('fasta'): ln -s '$type_of_scheme.scheme_input' '$type_of_scheme.scheme_input.name' && #end if @@ -112,7 +112,7 @@ $dev_args.use_json $input_files --scheme -#if $type_of_scheme.scheme_type == "custom": +#if $type_of_scheme.scheme_check == "custom": '$type_of_scheme.scheme_input.name' #else: $type_of_scheme.scheme_type @@ -189,19 +189,23 @@ </when> </conditional> <conditional name="type_of_scheme"> - <param name="scheme_type" type="select" - label="SNP Subtyping Scheme" - help="Select the SNP subtyping scheme you wish to subtype with"> - <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option> - <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option> - <option value="custom">Specify your own custom scheme</option> + <param name="scheme_check" type="select" + label="Subtyping Schemes" + help="Use included scheme or custom"> + <option value="standard">Included Biohansel Schemes</option> + <option value="custom">Select User Custom Scheme</option> </param> - <when value="heidelberg"/> - <when value="enteritidis"/> + <when value="standard"> + <param name="scheme_type" type="select" + label="Included SNP Subtyping Scheme"> + <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option> + <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option> + </param> + </when> <when value="custom"> <param name="scheme_input" type="data" format="fasta" - label="Your biohansel SNP Subtyping Scheme"/> + label="Your Custom Biohansel SNP Subtyping Scheme"/> </when> </conditional> <param name="subtype_metadata"