Mercurial > repos > thanhlv > data_manager_build_ariba_database
changeset 7:8a442938a61a draft
planemo upload for repository https://github.com/thanhleviet/galaxy-tools commit 98648bbb7796db528b5685d44a2a5b761c53c19b-dirty
| author | thanhlv |
|---|---|
| date | Sun, 19 May 2019 08:50:27 -0400 |
| parents | 6286fb2cadf5 |
| children | fb4da292b6d0 |
| files | data_manager/ariba_database_builder.xml |
| diffstat | 1 files changed, 8 insertions(+), 24 deletions(-) [+] |
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--- a/data_manager/ariba_database_builder.xml Sun May 19 08:42:37 2019 -0400 +++ b/data_manager/ariba_database_builder.xml Sun May 19 08:50:27 2019 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="ariba_database_builder" name="ARIBA build database" tool_type="manage_data" version="@VERSION@"> +<tool id="ariba_database_builder" name="ARIBA" tool_type="manage_data" version="@VERSION@"> <description>database builder</description> <macros> <import>macros.xml</import> @@ -8,27 +8,11 @@ <version_command>ariba version | head head -n 1</version_command> <command detect_errors="exit_code"> <![CDATA[ - #if str($library.lib_type) == "curated" - #set $library_ = str($library.curated) - #if str($library_) != 'None': - ariba getref '$library_' _tmp_db && ariba prepareref -f _tmp_db.fa -m _tmp_db.tsv '$library_' && - #end if + #if str($library.lib_type) != "fasta" + python '$__tool_directory__/ariba_data_base_builder.py' '${out_file}' -t $library.lib_type -d $library.db + #else + python '$__tool_directory__/ariba_data_base_builder.py' '${out_file}' -t $library.lib_type -d $library.db -c $library.coding -f $library.fasta #end if - - #if str($library.lib_type) == "mlst" - #set $library_ = str($library.curated) - #if str($library_) != 'None': - python '$__tool_directory__/mlst.py' '$library_' && - #end if - #end if - - #if str($library.lib_type) == "fasta" - #if str($library).fasta != 'None': - ariba prepareref --all_coding '$coding' -f '$library.fasta' '$library.db_name' - #end if - #end if - - python '$__tool_directory__/ariba_data_base_builder.py' --out '${out_file}' ]]> </command> <inputs> @@ -39,7 +23,7 @@ <option value="fasta">A fasta file</option> </param> <when value="curated"> - <param name="curated" type="select" multiple="false" label="Select partial library to download"> + <param name="db" type="select" multiple="false" label="Select partial library to download"> <option value="card">CARD</option> <option value="resfinder">Resfinder</option> <option value="plasmidfinder">Plasmidfinder</option> @@ -50,7 +34,7 @@ <option value="virulencefinder">virulencefinder</option> </param> <when value="mlst"> - <param name="mlst" type="select" multiple="false" label="Select a species"> + <param name="db" type="select" multiple="false" label="Select a species"> <option value="achs">Achromobacter spp.</option> <option value="acib1">Acinetobacter baumannii#1</option> <option value="acib2">Acinetobacter baumannii#2</option> @@ -197,7 +181,7 @@ </when> <when value="fasta"> <param name="fasta" type="data" format="fasta,fasta.gz" optional="false" /> - <param name="db_name" type="text" label="DB name" help = "The DB name should include no space and special characters" /> + <param name="db" type="text" label="DB name" help = "The DB name should include no space, special characters, and must be uniquely different to the name predefined in curated and mlst list" /> <param name="coding" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="Coding sequence?" /> </when> </conditional>