Mercurial > repos > jay > pdaug_peptide_data_access
changeset 7:24184ea66557 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
| author | jay |
|---|---|
| date | Sun, 09 Jan 2022 03:52:11 +0000 |
| parents | 92bdc5cbf028 |
| children | b67c1e1608c5 |
| files | PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.py PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml |
| diffstat | 2 files changed, 32 insertions(+), 8 deletions(-) [+] |
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--- a/PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.py Sun Jan 31 02:09:47 2021 +0000 +++ b/PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.py Sun Jan 09 03:52:11 2022 +0000 @@ -16,12 +16,12 @@ filterduplicates = subparsers.add_parser('filterduplicates') filterduplicates.add_argument("-I","--InFile", required=True, default=None, help="Input file") filterduplicates.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file") - +filterduplicates.add_argument("-A","--FilterAA", required=True, default=None, help="Filter amino acide") keepnaturalaa = subparsers.add_parser('keepnaturalaa') keepnaturalaa.add_argument("-I","--InFile", required=True, default=None, help="Inputt file") keepnaturalaa.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file") - +keepnaturalaa.add_argument("-A","--FilterAA", required=True, default=None, help="Filter amino acide") filteraa = subparsers.add_parser('filteraa') filteraa.add_argument("-I","--InFile", required=True, default=None, help="Input file")
--- a/PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml Sun Jan 31 02:09:47 2021 +0000 +++ b/PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml Sun Jan 09 03:52:11 2022 +0000 @@ -13,13 +13,29 @@ python '$__tool_directory__/PDAUG_Peptide_Data_Access.py' -d '$SelectDatasets.DataBaseType' -o '$output1' + #if $SelectDatasets.DataBaseType == "AMPvsTMP" + -d 'AMPvsTMP' + #end if + + #if $SelectDatasets.DataBaseType == "AMPvsUniProt" + -d 'AMPvsUniProt' + #end if + + #if $SelectDatasets.DataBaseType == "ACPvsTMP" + -d 'ACPvsTMP' + #end if + + #if $SelectDatasets.DataBaseType == "ACPvsRandom" + -d 'ACPvsRandom' + #end if + #if $SelectDatasets.DataBaseType == "query_apd" -L '$SelectDatasets.list1' #end if #if $SelectDatasets.DataBaseType == "query_camp" - -L '$SelectDatasets.list2' - #end if + -L '$SelectDatasets.list1' + #end if ]]></command> @@ -37,12 +53,20 @@ <option value="query_camp" > Query CAMP Database </option> </param> + <when value="AMPvsTMP"> + </when> + + <when value="AMPvsUniProt"> - <when value="AMPvsTMP"/> - <when value="AMPvsUniProt"/> - <when value="ACPvsTMP"/> - <when value="ACPvsRandom"/> + </when> + + <when value="ACPvsTMP"> + </when> + + <when value="ACPvsRandom"> + </when> + <when value="query_apd"> <param name="list1" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" /> </when>