Mercurial > repos > dchristiany > frogs_data_manager
diff data_manager/FROGS_data_manager.xml @ 10:238a5328279d draft
planemo upload commit b0ebe74a020dcb21b79d8d39e7b6a2f6533b2fc4-dirty
| author | dchristiany |
|---|---|
| date | Mon, 28 Oct 2019 06:46:53 -0400 |
| parents | 0d9cb5c5aa35 |
| children | 0cc5f020640e |
line wrap: on
line diff
--- a/data_manager/FROGS_data_manager.xml Mon Oct 07 10:56:23 2019 -0400 +++ b/data_manager/FROGS_data_manager.xml Mon Oct 28 06:46:53 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="FROGS_data_manager" name="FROGS Data manager" version="2019.10.07.1" tool_type="manage_data"> +<tool id="FROGS_data_manager" name="FROGS Data manager" version="2019.10.28" tool_type="manage_data"> <requirements> </requirements> <stdio> @@ -8,9 +8,16 @@ python $__tool_directory__/FROGS_data_manager.py --database="$database.database" #if $database.database=="frogs_db_data" - --custom_db="$database.db_type.custom_db" - --amplicons="$database.db_type.amplicons" + --all_dbs="$database.db_type.db" + #if $database.db_type.db=="false" + --date="$database.db_type.date" + --amplicons="$database.db_type.amplicons" + --bases="$database.db_type.bases" + --filters="$database.db_type.filters" + #end if + --only_last_versions="$database.only_last_versions" #end if + --tool_data="$__tool_data_path__" --output "$output" ]]></command> <inputs> @@ -21,47 +28,18 @@ </param> <when value="frogs_db_data"> <conditional name="db_type"> - <param name="custom_db" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Build a custom database"/> - <when value="true"> - <param name="amplicons" type="select" multiple="true"> - <option value="COI_MIDORI_MARINE_20180221">COI MIDORI MARINE 20180221</option> - <option value="COI_MIDORI_20180221">COI MIDORI 20180221</option> - <option value="COI_BOLD_1percentN_600nt_022019">COI BOLD 1percentN 600nt 022019</option> - <option value="COI_BOLD_1percentN_630nt_022019">COI BOLD 1percentN 630nt 022019</option> - <option value="ITS_UNITE_Euka_8.0">ITS UNITE Euka 8.0</option> - <option value="ITS_UNITE_Fungi_8.0">ITS UNITE Fungi 8.0</option> - <option value="COI_BOLD_022019">COI BOLD 022019</option> - <option value="COI_BOLD_1percentN_022019">COI BOLD 1percentN 022019</option> - <option value="EF1,18S_PHYMYCO-DB_2013">EF1,18S PHYMYCO-DB 2013</option> - <option value="16S_EZBioCloud_052018">16S EZBioCloud 052018</option> - <option value="18S_PR2_4.11.0">18S PR2 4.11.0</option> - <option value="16S_DAIRYdb_V1.1.2">16S DAIRYdb V1.1.2</option> - <option value="rbcL_Rsyst_Diatom_7">rbcL Rsyst Diatom 7</option> - <option value="ITS_UNITE_7.1">ITS UNITE 7.1</option> - <option value="rpoB_DB_NAME_TO_CHECK_122017">rpoB DB NAME TO CHECK 122017</option> - <option value="16S_SILVA_Pintail100_132">16S SILVA Pintail100 132</option> - <option value="16S_SILVA_Pintail50_132">16S SILVA Pintail50 132</option> - <option value="16S_SILVA_Pintail80_132">16S SILVA Pintail80 132</option> - <option value="16S_SILVA_132">16S SILVA 132</option> - <option value="18S_SILVA_132">18S SILVA 132</option> - <option value="23S_SILVA_132">23S SILVA 132</option> - <option value="16S_SILVA_Pintail100_128">16S SILVA Pintail100 128</option> - <option value="16S_SILVA_Pintail50_128">16S SILVA Pintail50 128</option> - <option value="16S_SILVA_Pintail80_128">16S SILVA Pintail80 128</option> - <option value="18S_PR2_Gb203_4.5">18S PR2 Gb203 4.5</option> - <option value="16S_MIDAS_S123_2.1.3">16S MIDAS S123 2.1.3</option> - <option value="16S_SILVA_128">16S SILVA 128</option> - <option value="18S_SILVA_123">18S SILVA 123</option> - <option value="18S_SILVA_128">18S SILVA 128</option> - <option value="23S_SILVA_128">23S SILVA 128</option> - <option value="16S_MIDAS_S119_1.20">16S MIDAS S119 1.20</option> - <option value="16S_Greengenes_13.5">16S Greengenes 13.5</option> - <option value="16S_SILVA_123">16S SILVA 123</option> - <option value="18S_SILVA_119-1">18S SILVA 119-1</option> - <option value="23S_SILVA_123">23S SILVA 123</option> + <param name="db" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Download all databases"/> + <when value="true"/> + <when value="false"> + <param name="date" value="0" type="text" label="Only more recent database than this date will be downloaded" help="Please enter a date at the following format: YYYYMMDD, leave 0 for no date"> + <validator type="regex" message="Please enter a date at the following format: YYYYMMDD, leave 0 for no date">0|[1-2]{1}[0-9]{3}[0-1]{1}[0-9]{1}([0-2]{1}[0-9]{1}|3[0-1]{1})</validator> </param> + <param name="amplicons" type="text" label='Select database to download by amplicons, put an amplicons list separated by "," ' help='example: "COI,ITS,16S" or "23S"'/> + <param name="bases" type="text" label='Select database to download by base, put a bases list separated by "," ' help='example: "SILVA,PR2,MIDAS" or "BOLD"'/> + <param name="filters" type="text" label='Select database to download by filters, put a filters list separated by "," ' help='example: "Pintail100,Fungi"'/> </when> </conditional> + <param name="only_last_versions" type="boolean" checked="true" label="Download only the last version of each database"/> </when> <when value="HVL_db_data"/> </conditional>