Mercurial > repos > galaxyp > percolator
changeset 3:abed51712ed0 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
| author | galaxyp |
|---|---|
| date | Sat, 08 Apr 2017 08:23:12 -0400 |
| parents | 7a0951d0e13e |
| children | 154147805a33 |
| files | nested_collection.py nested_collection.xml |
| diffstat | 2 files changed, 40 insertions(+), 23 deletions(-) [+] |
line wrap: on
line diff
--- a/nested_collection.py Fri Mar 10 03:20:52 2017 -0500 +++ b/nested_collection.py Sat Apr 08 08:23:12 2017 -0400 @@ -44,7 +44,7 @@ for batchcount, (pool_id, batch) in enumerate(get_batches_of_galaxyfiles( args.realnames, args.batchsize, args.poolids)): for fncount, batchfile in enumerate([args.galaxyfiles[index] for index in batch]): - dsetname = '{}_batch{}___inputfn{}.mzid'.format(pool_id, batchcount, fncount) + dsetname = '{}_batch{}___inputfn{}.data'.format(pool_id, batchcount, fncount) print('producing', dsetname) os.symlink(batchfile, dsetname)
--- a/nested_collection.xml Fri Mar 10 03:20:52 2017 -0500 +++ b/nested_collection.xml Sat Apr 08 08:23:12 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="batched_set_list_creator" name="Create nested list" version="3.1"> +<tool id="batched_set_list_creator" name="Create nested list" version="3.2"> <description>based on filenames and batch sizes</description> <stdio> <exit_code range="1:" /> @@ -24,6 +24,11 @@ </command> <inputs> <param name="batchsize" type="integer" optional="true" value="" label="Maximal amount of fractions to batch." help="No value means no maximum" /> + <param name="filetype" type="select" label="Which datatype to nest?"> + <option value="mzid">mzIdentML</option> + <option value="percout">Percolator out</option> + <option value="tabular">Tabular</option> + </param> <repeat name="poolids" title="Batch pools" help="Pools containing batches (optional, not using this will result in one pool)"> <param name="pool_identifier" type="text" label="Filename part identifying batchpool" help="Specify part of the input filenames that are unique for each pool, e.g set_A. Do not use 3 consecutive underscores."/> @@ -31,13 +36,23 @@ <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" /> </inputs> <outputs> - <collection name="batched_fractions" type="list:list" label="Pooled batched data"> - <discover_datasets pattern="(?P<identifier_0>\w+[^_][^_][^_])___(?P<identifier_1>[^_]+)\.mzid" ext="mzid" visible="true" /> + <collection name="batched_fractions_mzid" type="list:list" label="Pooled batched mzIdentML data"> + <filter>filetype == "mzid"</filter> + <discover_datasets pattern="(?P<identifier_0>\w+[^_][^_][^_])___(?P<identifier_1>[^_]+)\.data" ext="mzid" visible="false" /> + </collection> + <collection name="batched_fractions_perco" type="list:list" label="Pooled batched percolator data"> + <filter>filetype == "percout"</filter> + <discover_datasets pattern="(?P<identifier_0>\w+[^_][^_][^_])___(?P<identifier_1>[^_]+)\.data" ext="percout" visible="false" /> + </collection> + <collection name="batched_fractions_tab" type="list:list" label="Pooled batched tabular data"> + <filter>filetype == "tabular"</filter> + <discover_datasets pattern="(?P<identifier_0>\w+[^_][^_][^_])___(?P<identifier_1>[^_]+)\.data" ext="tabular" visible="false" /> </collection> </outputs> <tests> <test> <param name="batchsize" value="2"/> + <param name="filetype" value="mzid" /> <param name="listtobatch"> <collection type="list"> <element name="fraction_one_spectra" value="empty_file1.mzid"/> @@ -46,14 +61,14 @@ <element name="fraction_four_spectra" value="empty_file4.mzid"/> </collection> </param> - <output_collection name="batched_fractions" type="list:list"> + <output_collection name="batched_fractions_mzid" type="list:list"> <element name="pool0_batch0"> - <element name="inputfn0" file="empty_file1.mzid"/> - <element name="inputfn1" file="empty_file2.mzid"/> + <element name="inputfn0" ftype="mzid" file="empty_file1.mzid"/> + <element name="inputfn1" ftype="mzid" file="empty_file2.mzid"/> </element> <element name="pool0_batch1"> - <element name="inputfn0" file="empty_file3.mzid"/> - <element name="inputfn1" file="empty_file4.mzid"/> + <element name="inputfn0" ftype="mzid" file="empty_file3.mzid"/> + <element name="inputfn1" ftype="mzid" file="empty_file4.mzid"/> </element> </output_collection> </test> @@ -64,6 +79,7 @@ <repeat name="poolids"> <param name="pool_identifier" value="set2"/> </repeat> + <param name="filetype" value="tabular" /> <param name="listtobatch"> <collection type="list"> <element name="fr_one_set1_spectra" value="empty_file1.mzid"/> @@ -74,16 +90,16 @@ <element name="fr_three_set2_spectra" value="empty_file6.mzid"/> </collection> </param> - <output_collection name="batched_fractions" type="list:list"> + <output_collection name="batched_fractions_tab" type="list:list"> <element name="set1_batch0"> - <element name="inputfn0" file="empty_file1.mzid"/> - <element name="inputfn1" file="empty_file2.mzid"/> - <element name="inputfn2" file="empty_file3.mzid"/> + <element name="inputfn0" ftype="tabular" file="empty_file1.mzid"/> + <element name="inputfn1" ftype="tabular" file="empty_file2.mzid"/> + <element name="inputfn2" ftype="tabular" file="empty_file3.mzid"/> </element> <element name="set2_batch1"> - <element name="inputfn0" file="empty_file4.mzid"/> - <element name="inputfn1" file="empty_file5.mzid"/> - <element name="inputfn2" file="empty_file6.mzid"/> + <element name="inputfn0" ftype="tabular" file="empty_file4.mzid"/> + <element name="inputfn1" ftype="tabular" file="empty_file5.mzid"/> + <element name="inputfn2" ftype="tabular" file="empty_file6.mzid"/> </element> </output_collection> </test> @@ -95,6 +111,7 @@ <repeat name="poolids"> <param name="pool_identifier" value="set2"/> </repeat> + <param name="filetype" value="percout" /> <param name="listtobatch"> <collection type="list"> <element name="fr_one_set1_spectra" value="empty_file1.mzid"/> @@ -105,20 +122,20 @@ <element name="fr_three_set2_spectra" value="empty_file6.mzid"/> </collection> </param> - <output_collection name="batched_fractions" type="list:list"> + <output_collection name="batched_fractions_perco" type="list:list"> <element name="set1_batch0"> - <element name="inputfn0" file="empty_file1.mzid"/> - <element name="inputfn1" file="empty_file2.mzid"/> + <element name="inputfn0" ftype="percout" file="empty_file1.mzid"/> + <element name="inputfn1" ftype="percout" file="empty_file2.mzid"/> </element> <element name="set1_batch1"> - <element name="inputfn0" file="empty_file3.mzid"/> + <element name="inputfn0" ftype="percout" file="empty_file3.mzid"/> </element> <element name="set2_batch2"> - <element name="inputfn0" file="empty_file4.mzid"/> - <element name="inputfn1" file="empty_file5.mzid"/> + <element name="inputfn0" ftype="percout" file="empty_file4.mzid"/> + <element name="inputfn1" ftype="percout" file="empty_file5.mzid"/> </element> <element name="set2_batch3"> - <element name="inputfn0" file="empty_file6.mzid"/> + <element name="inputfn0" ftype="percout" file="empty_file6.mzid"/> </element> </output_collection> </test>