# HG changeset patch
# User galaxyp
# Date 1507316429 14400
# Node ID 8240d0714a97249f0f30a484f089dc0ff0d6183e
# Parent 1881935e53514ee0a5a26dc60d2a5c7fdbd5bd35
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
diff -r 1881935e5351 -r 8240d0714a97 COPYING
--- a/COPYING Wed Feb 01 20:53:23 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,121 +0,0 @@
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diff -r 1881935e5351 -r 8240d0714a97 README.md
--- a/README.md Wed Feb 01 20:53:23 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-GalaxyP - MyriMatch
-===================
-
-* Home:
-* Galaxy Tool Shed:
-* Tool ID: `myrimatch`
-
-
-Description
------------
-
-Bumbershoot MyriMatch.
-
-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
- Vanderbilt University Medical Center
-
-* John Chilton
- Minnesota Supercomputing Institute, Univeristy of Minnesota
diff -r 1881935e5351 -r 8240d0714a97 macros.xml
--- a/macros.xml Wed Feb 01 20:53:23 2017 -0500
+++ b/macros.xml Fri Oct 06 15:00:29 2017 -0400
@@ -1,8 +1,8 @@
- 3.0.10246
+ 3.0.11392
- bumbershoot
+ bumbershoot
diff -r 1881935e5351 -r 8240d0714a97 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 Fri Oct 06 15:00:29 2017 -0400
@@ -0,0 +1,20 @@
+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 1881935e5351 -r 8240d0714a97 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 Fri Oct 06 15:00:29 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 1881935e5351 -r 8240d0714a97 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 Fri Oct 06 15:00:29 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 1881935e5351 -r 8240d0714a97 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 Fri Oct 06 15:00:29 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 1881935e5351 -r 8240d0714a97 test-data/201203-624176-12-mm-gui-test.idpDB
Binary file test-data/201203-624176-12-mm-gui-test.idpDB has changed
diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-cm-filtered.idpDB
Binary file test-data/201208-378803-cm-filtered.idpDB has changed
diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-cm.idpDB
Binary file test-data/201208-378803-cm.idpDB has changed
diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-cm.pep.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201208-378803-cm.pep.xml Fri Oct 06 15:00:29 2017 -0400
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diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-embeddedGenes.idpDB
Binary file test-data/201208-378803-embeddedGenes.idpDB has changed
diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-embeddedGenesAndQuantitation.idpDB
Binary file test-data/201208-378803-embeddedGenesAndQuantitation.idpDB has changed
diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-embeddedGenesAndScanTimes.idpDB
Binary file test-data/201208-378803-embeddedGenesAndScanTimes.idpDB has changed
diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-embeddedGenesAndSpectra.idpDB
Binary file test-data/201208-378803-embeddedGenesAndSpectra.idpDB has changed
diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-embeddedGenesAndSpectra2.idpDB
Binary file test-data/201208-378803-embeddedGenesAndSpectra2.idpDB has changed
diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-mm-filtered.idpDB
Binary file test-data/201208-378803-mm-filtered.idpDB has changed
diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-mm.idpDB
Binary file test-data/201208-378803-mm.idpDB has changed
diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-msgf-filtered.idpDB
Binary file test-data/201208-378803-msgf-filtered.idpDB has changed
diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-msgf.idpDB
Binary file test-data/201208-378803-msgf.idpDB has changed
diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803-msgf.mzid
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201208-378803-msgf.mzid Fri Oct 06 15:00:29 2017 -0400
@@ -0,0 +1,4631 @@
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diff -r 1881935e5351 -r 8240d0714a97 test-data/201208-378803.idpDB
Binary file test-data/201208-378803.idpDB has changed