# HG changeset patch
# User galaxyp
# Date 1503529868 14400
# Node ID 925ec25a54368257914f443b100d5bb1368eddfe
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
diff -r 000000000000 -r 925ec25a5436 COPYING
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING Wed Aug 23 19:11:08 2017 -0400
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+of the License, and in such case Affirmer hereby affirms that he or she
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diff -r 000000000000 -r 925ec25a5436 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Wed Aug 23 19:11:08 2017 -0400
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+GalaxyP - idpQuery
+====================
+
+* Home:
+* Galaxy Tool Shed:
+* Tool ID: `idpquery`
+
+
+Description
+-----------
+
+Bumbershoot idpQuery, a part of Bumbershoot IDPicker.
+
+See:
+
+*
+
+
+GalaxyP Community
+-----------------
+
+Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at:
+
+
+
+
+License
+-------
+
+Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
+
+To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
+
+You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see .
+
+You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
+
+
+Contributing
+------------
+
+Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in
+
+
+Authors
+-------
+
+Authors and contributors:
+
+* Matt Chambers
+
+* John Chilton
+ Minnesota Supercomputing Institute, University of Minnesota
\ No newline at end of file
diff -r 000000000000 -r 925ec25a5436 idpquery.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/idpquery.xml Wed Aug 23 19:11:08 2017 -0400
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+
+
+ Creates text reports from idpDB files.
+
+ macros.xml
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+ 10.1021/pr900360j
+ @misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
+ year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}
+
+
diff -r 000000000000 -r 925ec25a5436 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Aug 23 19:11:08 2017 -0400
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+
+ 3.0.10246
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+ bumbershoot
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diff -r 000000000000 -r 925ec25a5436 test-data/201203-624176-12-mm-gui-test-Gene-GeneId,Accession,DistinctPeptides.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201203-624176-12-mm-gui-test-Gene-GeneId,Accession,DistinctPeptides.tsv Wed Aug 23 19:11:08 2017 -0400
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+GeneId Accession DistinctPeptides
+Unmapped_gi|165973958|ref|NP_001107199.1| gi|165973958|ref|NP_001107199.1| 2
+Unmapped_gi|27806851|ref|NP_776358.1| gi|27806851|ref|NP_776358.1| 21
+Unmapped_gi|27806963|ref|NP_776953.1| gi|27806963|ref|NP_776953.1| 2
+Unmapped_gi|27807109|ref|NP_777040.1| gi|27807109|ref|NP_777040.1| 7
+Unmapped_gi|30466252|ref|NP_848667.1| gi|30466252|ref|NP_848667.1| 16
+Unmapped_gi|30794280|ref|NP_851335.1| gi|30794280|ref|NP_851335.1| 29
+Unmapped_gi|30794348|ref|NP_851372.1| gi|30794348|ref|NP_851372.1| 13
+Unmapped_gi|32880221|ref|NP_872593.1| gi|32880221|ref|NP_872593.1| 21
+Unmapped_gi|528903801|ref|XP_871686.4| gi|528903801|ref|XP_871686.4| 2
+Unmapped_gi|528935739|ref|XP_005201142.1| gi|528935739|ref|XP_005201142.1| 7
+Unmapped_gi|528947854|ref|XP_002687054.3| gi|528947854|ref|XP_002687054.3| 2
+Unmapped_gi|528953234|ref|XP_005208080.1| gi|528953234|ref|XP_005208080.1| 13
+Unmapped_gi|528953238|ref|XP_005208082.1| gi|528953238|ref|XP_005208082.1| 13
+Unmapped_gi|528953240|ref|XP_005208083.1| gi|528953240|ref|XP_005208083.1| 13
+Unmapped_gi|528969819|ref|XP_005213230.1| gi|528969819|ref|XP_005213230.1| 18
+Unmapped_gi|528993971|ref|XP_005219929.1| gi|528993971|ref|XP_005219929.1| 21
+Unmapped_gi|528993973|ref|XP_005219930.1| gi|528993973|ref|XP_005219930.1| 21
+Unmapped_gi|528993975|ref|XP_005219931.1| gi|528993975|ref|XP_005219931.1| 21
+Unmapped_gi|87196497|ref|NP_776354.2| gi|87196497|ref|NP_776354.2| 18
diff -r 000000000000 -r 925ec25a5436 test-data/201203-624176-12-mm-gui-test-GeneGroup-GeneGroup,GeneId,DistinctMatches.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201203-624176-12-mm-gui-test-GeneGroup-GeneGroup,GeneId,DistinctMatches.tsv Wed Aug 23 19:11:08 2017 -0400
@@ -0,0 +1,10 @@
+GeneGroup GeneId DistinctMatches
+1 Unmapped_gi|27806963|ref|NP_776953.1| 2
+2 Unmapped_gi|30466252|ref|NP_848667.1| 29
+3 Unmapped_gi|30794280|ref|NP_851335.1| 43
+4 Unmapped_gi|32880221|ref|NP_872593.1| 27
+5 Unmapped_gi|528935739|ref|XP_005201142.1|,Unmapped_gi|27807109|ref|NP_777040.1| 9
+6 Unmapped_gi|528903801|ref|XP_871686.4|,Unmapped_gi|528947854|ref|XP_002687054.3|,Unmapped_gi|165973958|ref|NP_001107199.1| 4
+7 Unmapped_gi|528953234|ref|XP_005208080.1|,Unmapped_gi|528953238|ref|XP_005208082.1|,Unmapped_gi|528953240|ref|XP_005208083.1|,Unmapped_gi|30794348|ref|NP_851372.1| 17
+8 Unmapped_gi|528993971|ref|XP_005219929.1|,Unmapped_gi|528993973|ref|XP_005219930.1|,Unmapped_gi|528993975|ref|XP_005219931.1|,Unmapped_gi|27806851|ref|NP_776358.1| 27
+9 Unmapped_gi|528969819|ref|XP_005213230.1|,Unmapped_gi|87196497|ref|NP_776354.2| 33
diff -r 000000000000 -r 925ec25a5436 test-data/201203-624176-12-mm-gui-test-Protein-Accession,FilteredSpectra,Description.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201203-624176-12-mm-gui-test-Protein-Accession,FilteredSpectra,Description.tsv Wed Aug 23 19:11:08 2017 -0400
@@ -0,0 +1,20 @@
+Accession FilteredSpectra Description
+gi|528903801|ref|XP_871686.4| 4 PREDICTED: cationic trypsin isoformX1 [Bos taurus]
+gi|528935739|ref|XP_005201142.1| 10 PREDICTED: superoxide dismutase [Cu-Zn] isoform X1 [Bos taurus]
+gi|528947854|ref|XP_002687054.3| 4 PREDICTED: cationic trypsin isoform X1 [Bos taurus]
+gi|528953234|ref|XP_005208080.1| 20 PREDICTED: alpha-S1-casein isoform X1 [Bos taurus]
+gi|528953238|ref|XP_005208082.1| 20 PREDICTED: alpha-S1-casein isoform X3 [Bos taurus]
+gi|528953240|ref|XP_005208083.1| 20 PREDICTED: alpha-S1-casein isoform X4 [Bos taurus]
+gi|528969819|ref|XP_005213230.1| 36 PREDICTED: beta-lactoglobulin isoform X1 [Bos taurus]
+gi|528993971|ref|XP_005219929.1| 29 PREDICTED: lactoperoxidase isoform X1 [Bos taurus]
+gi|528993973|ref|XP_005219930.1| 29 PREDICTED: lactoperoxidase isoform X2 [Bos taurus]
+gi|528993975|ref|XP_005219931.1| 29 PREDICTED: lactoperoxidase isoform X3 [Bos taurus]
+gi|30794280|ref|NP_851335.1| 43 serum albumin precursor [Bos taurus]
+gi|30794348|ref|NP_851372.1| 20 alpha-S1-casein precursor [Bos taurus]
+gi|87196497|ref|NP_776354.2| 36 beta-lactoglobulin precursor [Bos taurus]
+gi|165973958|ref|NP_001107199.1| 4 cationic trypsin precursor [Bos taurus]
+gi|27807109|ref|NP_777040.1| 10 superoxide dismutase [Cu-Zn] [Bos taurus]
+gi|27806963|ref|NP_776953.1| 2 alpha-S2-casein precursor [Bos taurus]
+gi|30466252|ref|NP_848667.1| 31 carbonic anhydrase 2 [Bos taurus]
+gi|32880221|ref|NP_872593.1| 32 glutamate dehydrogenase 1, mitochondrial precursor [Bos taurus]
+gi|27806851|ref|NP_776358.1| 29 lactoperoxidase precursor [Bos taurus]
diff -r 000000000000 -r 925ec25a5436 test-data/201203-624176-12-mm-gui-test-ProteinGroup-ProteinGroup,Accession,PercentCoverage.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201203-624176-12-mm-gui-test-ProteinGroup-ProteinGroup,Accession,PercentCoverage.tsv Wed Aug 23 19:11:08 2017 -0400
@@ -0,0 +1,10 @@
+ProteinGroup Accession PercentCoverage
+1 gi|30794280|ref|NP_851335.1| 42.01
+2 gi|30466252|ref|NP_848667.1| 39.23
+3 gi|32880221|ref|NP_872593.1| 35.84
+4 gi|27806963|ref|NP_776953.1| 7.21
+5 gi|528969819|ref|XP_005213230.1|,gi|87196497|ref|NP_776354.2| 56.18
+6 gi|528993971|ref|XP_005219929.1|,gi|528993973|ref|XP_005219930.1|,gi|528993975|ref|XP_005219931.1|,gi|27806851|ref|NP_776358.1| 28.09
+7 gi|528903801|ref|XP_871686.4|,gi|528947854|ref|XP_002687054.3|,gi|165973958|ref|NP_001107199.1| 12.6
+8 gi|528953234|ref|XP_005208080.1|,gi|528953238|ref|XP_005208082.1|,gi|528953240|ref|XP_005208083.1|,gi|30794348|ref|NP_851372.1| 41.59
+9 gi|528935739|ref|XP_005201142.1|,gi|27807109|ref|NP_777040.1| 33.55
diff -r 000000000000 -r 925ec25a5436 test-data/201203-624176-12-mm-gui-test.idpDB
Binary file test-data/201203-624176-12-mm-gui-test.idpDB has changed