Mercurial > repos > erasmus-medical-center > hla_dq
changeset 1:4fc47a3ff9e8 draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit 3f631031b57350f0437e90e4de3352725bb84716
| author | erasmus-medical-center |
|---|---|
| date | Wed, 30 May 2018 09:21:15 -0400 |
| parents | 10a407fb5072 |
| children | |
| files | hla_dq.py hla_dq.xml test-data/test1_results.tsv test-data/test2_results.tsv |
| diffstat | 4 files changed, 13 insertions(+), 13 deletions(-) [+] |
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--- a/hla_dq.py Wed May 30 07:50:21 2018 -0400 +++ b/hla_dq.py Wed May 30 09:21:15 2018 -0400 @@ -42,12 +42,12 @@ ''' each combination of DQA1,DQB1,type ''' associated_combinations = [ - ['02:01', '02:02', 'DQ2.2'], - ['03:03', '02:02', 'DQ2.3'], - ['05:01', '02:01', 'DQ2.5'], - ['03:01', '03:02', 'DQ8'], - ['03:02', '03:02', 'DQ8'], - ['03:03', '03:02', 'DQ8']] + ['02:01', '02:02', ' DQ2.2 (02:01-02:02)'], + ['03:03', '02:02', ' DQ2.3 (03:03-02:02)'], + ['05:01', '02:01', ' DQ2.5 (05:01-02:01)'], + ['03:01', '03:02', ' DQ8 (03:01-03:02)'], + ['03:02', '03:02', ' DQ8 (03:02-03:02)'], + ['03:03', '03:02', ' DQ8 (03:03-03:02)']] return [a[2] for a in associated_combinations if a[0] in typesA and a[1] in typesB] @@ -83,4 +83,4 @@ outfile.write( 'A' + str(bcount) + '\t' + '\t'.join([';'.join(sorted(set(l))) - if l else '-' for l in line])+'\n') + if l else ' -' for l in line])+'\n')
--- a/hla_dq.xml Wed May 30 07:50:21 2018 -0400 +++ b/hla_dq.xml Wed May 30 09:21:15 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="hla_dq" name="HLA-DQ typing" version="1.0"> +<tool id="hla_dq" name="HLA-DQ typing" version="1.1"> <description> Determine possible associated types given BLAST IMGT/HLA annotation</description> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/hla_dq.py'
--- a/test-data/test1_results.tsv Wed May 30 07:50:21 2018 -0400 +++ b/test-data/test1_results.tsv Wed May 30 09:21:15 2018 -0400 @@ -1,3 +1,3 @@ B1 B2 -A1 - - -A2 - DQ8 +A1 - - +A2 - DQ8 (03:01-03:02)
--- a/test-data/test2_results.tsv Wed May 30 07:50:21 2018 -0400 +++ b/test-data/test2_results.tsv Wed May 30 09:21:15 2018 -0400 @@ -1,4 +1,4 @@ B1 B2 B3 -A1 - - DQ2.2 -A2 - DQ8 DQ8 -A3 - DQ8 DQ2.2;DQ2.3;DQ2.5;DQ8 +A1 - - DQ2.2 (02:01-02:02) +A2 - DQ8 (03:01-03:02) DQ8 (03:01-03:02) +A3 - DQ8 (03:01-03:02); DQ8 (03:02-03:02); DQ8 (03:03-03:02) DQ2.2 (02:01-02:02); DQ2.3 (03:03-02:02); DQ2.5 (05:01-02:01); DQ8 (03:01-03:02); DQ8 (03:02-03:02); DQ8 (03:03-03:02)