# HG changeset patch
# User galaxyp
# Date 1597305213 14400
# Node ID 07107a686ce9ab9772d43ed81da9e812862f6190
# Parent dce55ca21b9879f4d130a7d26d16448e2b396788
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit de8cdf895c3c6113f301a119788701b2465a1b1b"
diff -r dce55ca21b98 -r 07107a686ce9 nested_collection.py
--- a/nested_collection.py Fri May 19 09:01:27 2017 -0400
+++ b/nested_collection.py Thu Aug 13 03:53:33 2020 -0400
@@ -57,5 +57,6 @@
print('producing', dsetname)
os.symlink(args.galaxyfiles[fnindex], dsetname)
+
if __name__ == '__main__':
main()
diff -r dce55ca21b98 -r 07107a686ce9 nested_collection.xml
--- a/nested_collection.xml Fri May 19 09:01:27 2017 -0400
+++ b/nested_collection.xml Thu Aug 13 03:53:33 2020 -0400
@@ -82,7 +82,7 @@
-
+
diff -r dce55ca21b98 -r 07107a686ce9 percolator.xml
--- a/percolator.xml Fri May 19 09:01:27 2017 -0400
+++ b/percolator.xml Thu Aug 13 03:53:33 2020 -0400
@@ -1,8 +1,9 @@
-
+
accurate peptide identification
-
- percolator
-
+
+ percolator_macros.xml
+
+
diff -r dce55ca21b98 -r 07107a686ce9 percolator_converters.xml
--- a/percolator_converters.xml Fri May 19 09:01:27 2017 -0400
+++ b/percolator_converters.xml Thu Aug 13 03:53:33 2020 -0400
@@ -1,8 +1,9 @@
-
+
to create Percolator input files
-
- percolator
-
+
+ percolator_macros.xml
+
+
diff -r dce55ca21b98 -r 07107a686ce9 percolator_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/percolator_macros.xml Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,9 @@
+
+ 3.5
+
+
+ percolator
+
+
+
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file1.mzid
--- a/test-data/empty_file1.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file1.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file10.mzid
--- a/test-data/empty_file10.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file10.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file11.mzid
--- a/test-data/empty_file11.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file11.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file12.mzid
--- a/test-data/empty_file12.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file12.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file13.mzid
--- a/test-data/empty_file13.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file13.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file14.mzid
--- a/test-data/empty_file14.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file14.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file2.mzid
--- a/test-data/empty_file2.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file2.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file3.mzid
--- a/test-data/empty_file3.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file3.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file4.mzid
--- a/test-data/empty_file4.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file4.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file5.mzid
--- a/test-data/empty_file5.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file5.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file6.mzid
--- a/test-data/empty_file6.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file6.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file7.mzid
--- a/test-data/empty_file7.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file7.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file8.mzid
--- a/test-data/empty_file8.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file8.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/empty_file9.mzid
--- a/test-data/empty_file9.mzid Fri May 19 09:01:27 2017 -0400
+++ b/test-data/empty_file9.mzid Thu Aug 13 03:53:33 2020 -0400
@@ -0,0 +1,1 @@
+
diff -r dce55ca21b98 -r 07107a686ce9 test-data/percolatorInresult.txt
--- a/test-data/percolatorInresult.txt Fri May 19 09:01:27 2017 -0400
+++ b/test-data/percolatorInresult.txt Thu Aug 13 03:53:33 2020 -0400
@@ -1,3 +1,3 @@
SpecId Label ScanNr ExpMass CalcMass RawScore DeNovoScore ScoreRatio Energy lnEValue IsotopeError lnExplainedIonCurrentRatio lnNTermIonCurrentRatio lnCTermIonCurrentRatio lnMS2IonCurrent Mass PepLen dM absdM MeanErrorTop7 sqMeanErrorTop7 StdevErrorTop7 Charge2 Charge3 Charge4 Charge5 enzN enzC enzInt ptm Peptide Proteins
DefaultDirection - - - - 0 -1 0 -2 6 -2.5 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0
-decoy_SII_80_1_180_3_1 -1 180 1501.37 1501.04 -131 22 -1 153 -9.16055 1 -3.23882 -9.21034 -3.23882 10.4876 1501.37 33 -2.96829e-06 2.96829e-06 28.587 51.0759 28.587 0 1 0 0 1 1 2 5 K.[UNIMOD:737]LRPAFRQC[UNIMOD:4]C[UNIMOD:4]YELHAGELGWYIMENYFSLEC[UNIMOD:4]M[UNIMOD:35]RR.D decoy_ENSP00000304127 decoy_ENSP00000378424
+decoy_SII_80_1_180_3_1 -1 180 1501.37 1501.04 -131 22 -1 153 -9.16055 1 -3.23882 -9.21034 -3.23882 10.4876 1501.37 33 -4.53912e-06 4.53912e-06 28.587 51.0759 28.587 0 1 0 0 1 1 2 5 K.[UNIMOD:737]LRPAFRQC[UNIMOD:4]C[UNIMOD:4]YELHAGELGWYIMENYFSLEC[UNIMOD:4]M[UNIMOD:35]RR.D decoy_ENSP00000304127 decoy_ENSP00000378424
diff -r dce55ca21b98 -r 07107a686ce9 test-data/percolatorInresult_multifractions.txt
--- a/test-data/percolatorInresult_multifractions.txt Fri May 19 09:01:27 2017 -0400
+++ b/test-data/percolatorInresult_multifractions.txt Thu Aug 13 03:53:33 2020 -0400
@@ -1,4 +1,4 @@
SpecId Label ScanNr ExpMass CalcMass RawScore DeNovoScore ScoreRatio Energy lnEValue IsotopeError lnExplainedIonCurrentRatio lnNTermIonCurrentRatio lnCTermIonCurrentRatio lnMS2IonCurrent Mass PepLen dM absdM MeanErrorTop7 sqMeanErrorTop7 StdevErrorTop7 Charge2 Charge3 Charge4 Charge5 enzN enzC enzInt ptm Peptide Proteins
DefaultDirection - - - - 0 -1 0 -2 6 -2.5 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0
-decoy_SII_80_1_180_3_1 -1 180 1501.37 1501.04 -131 22 -1 153 -9.16055 1 -3.23882 -9.21034 -3.23882 10.4876 1501.37 33 -2.96829e-06 2.96829e-06 28.587 51.0759 28.587 0 1 0 0 1 1 2 5 K.[UNIMOD:737]LRPAFRQC[UNIMOD:4]C[UNIMOD:4]YELHAGELGWYIMENYFSLEC[UNIMOD:4]M[UNIMOD:35]RR.D decoy_ENSP00000304127 decoy_ENSP00000378424
-decoy_SII_80_1_180_3_1 -1 180 1501.37 1501.04 -131 22 -1 153 -9.16055 1 -3.23882 -9.21034 -3.23882 10.4876 1501.37 33 -2.96829e-06 2.96829e-06 28.587 51.0759 28.587 0 1 0 0 1 1 2 5 K.[UNIMOD:737]LRPAFRQC[UNIMOD:4]C[UNIMOD:4]YELHAGELGWYIMENYFSLEC[UNIMOD:4]M[UNIMOD:35]RR.D decoy_ENSP00000304127 decoy_ENSP00000378424
+decoy1_SII_80_1_180_3_1 -1 180 1501.37 1501.04 -131 22 -1 153 -9.16055 1 -3.23882 -9.21034 -3.23882 10.4876 1501.37 33 -4.53912e-06 4.53912e-06 28.587 51.0759 28.587 0 1 0 0 1 1 2 5 K.[UNIMOD:737]LRPAFRQC[UNIMOD:4]C[UNIMOD:4]YELHAGELGWYIMENYFSLEC[UNIMOD:4]M[UNIMOD:35]RR.D decoy_ENSP00000304127 decoy_ENSP00000378424
+decoy2_SII_80_1_180_3_1 -1 180 1501.37 1501.04 -131 22 -1 153 -9.16055 1 -3.23882 -9.21034 -3.23882 10.4876 1501.37 33 -4.53912e-06 4.53912e-06 28.587 51.0759 28.587 0 1 0 0 1 1 2 5 K.[UNIMOD:737]LRPAFRQC[UNIMOD:4]C[UNIMOD:4]YELHAGELGWYIMENYFSLEC[UNIMOD:4]M[UNIMOD:35]RR.D decoy_ENSP00000304127 decoy_ENSP00000378424
diff -r dce55ca21b98 -r 07107a686ce9 test-data/percolatorOut.xml
--- a/test-data/percolatorOut.xml Fri May 19 09:01:27 2017 -0400
+++ b/test-data/percolatorOut.xml Thu Aug 13 03:53:33 2020 -0400
@@ -4,10 +4,10 @@
xmlns:p="http://per-colator.com/percolator_out/15"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://per-colator.com/percolator_out/15 https://github.com/percolator/percolator/raw/pout-1-5/src/xml/percolator_out.xsd"
-p:majorVersion="3" p:minorVersion="01" p:percolator_version="Percolator version 3.01">
+p:majorVersion="3" p:minorVersion="05" p:percolator_version="Percolator version 3.05.0">
- percolator -X percotest -j percolatorTab --decoy-xml-output
+ percolator -j percolatorTab -X percotest --decoy-xml-output -y
0.790264
0.805704
@@ -19,7 +19,7 @@
0.000000
2.195178e-02
- 6.523451e-02
+ 4.817157e-02
1111.0600
1111.070
@@ -30,7 +30,7 @@
0.000
2.195e-02
- 6.523e-02
+ 4.817e-02
573.8040
573.810
@@ -43,7 +43,7 @@
0.000
2.195e-02
- 6.523e-02
+ 4.817e-02
804.7940
804.802
@@ -67,7 +67,7 @@
-0.017
2.195e-02
- 7.098e-02
+ 5.255e-02
1020.5000
1020.180
@@ -79,7 +79,7 @@
-0.023
2.195e-02
- 7.318e-02
+ 5.422e-02
568.2950
568.100
@@ -90,7 +90,7 @@
-0.230
2.195e-02
- 2.088e-01
+ 1.597e-01
538.5580
538.563
@@ -124,7 +124,7 @@
-0.234
2.195e-02
- 2.127e-01
+ 1.628e-01
700.0860
700.093
@@ -141,7 +141,7 @@
-0.236
2.195e-02
- 2.152e-01
+ 1.648e-01
1023.0400
1023.050
@@ -151,7 +151,7 @@
-0.280
2.195e-02
- 2.678e-01
+ 2.065e-01
973.1370
973.145
@@ -162,7 +162,7 @@
-0.285
2.195e-02
- 2.756e-01
+ 2.126e-01
1128.0700
1127.580
@@ -177,7 +177,7 @@
-0.289
2.195e-02
- 2.805e-01
+ 2.165e-01
939.5320
939.540
@@ -189,7 +189,7 @@
-0.289
2.195e-02
- 2.809e-01
+ 2.168e-01
897.9910
898.000
@@ -203,7 +203,7 @@
-0.324
2.195e-02
- 3.348e-01
+ 2.599e-01
719.1310
719.138
@@ -233,7 +233,7 @@
-0.329
2.195e-02
- 3.436e-01
+ 2.670e-01
525.2790
525.284
@@ -246,7 +246,7 @@
-0.342
2.195e-02
- 3.660e-01
+ 2.849e-01
1086.5600
1086.570
@@ -256,7 +256,7 @@
-0.344
2.195e-02
- 3.700e-01
+ 2.881e-01
831.1240
831.132
@@ -266,7 +266,7 @@
-0.351
2.195e-02
- 3.841e-01
+ 2.995e-01
863.0590
862.732
@@ -278,7 +278,7 @@
-0.354
2.195e-02
- 3.898e-01
+ 3.040e-01
876.4500
876.456
@@ -290,7 +290,7 @@
-0.357
2.195e-02
- 3.942e-01
+ 3.076e-01
1094.5500
1094.560
@@ -300,7 +300,7 @@
-0.377
2.195e-02
- 4.356e-01
+ 3.410e-01
950.4940
950.502
@@ -312,7 +312,7 @@
-0.380
2.195e-02
- 4.428e-01
+ 3.468e-01
736.4180
736.425
@@ -322,7 +322,7 @@
-0.382
2.195e-02
- 4.487e-01
+ 3.515e-01
526.6090
526.614
@@ -337,7 +337,7 @@
-0.391
2.195e-02
- 4.679e-01
+ 3.671e-01
855.7670
855.774
@@ -363,7 +363,7 @@
-0.400
2.195e-02
- 4.907e-01
+ 3.856e-01
967.5510
967.559
@@ -375,7 +375,7 @@
-0.402
2.195e-02
- 4.957e-01
+ 3.896e-01
837.4880
837.496
@@ -386,7 +386,7 @@
-0.405
2.195e-02
- 5.026e-01
+ 3.953e-01
823.9180
823.925
@@ -397,7 +397,7 @@
-0.436
2.195e-02
- 5.865e-01
+ 4.636e-01
981.0370
981.046
@@ -407,7 +407,7 @@
-0.452
2.195e-02
- 6.348e-01
+ 5.031e-01
368.8160
368.819
@@ -418,7 +418,7 @@
-0.453
2.195e-02
- 6.376e-01
+ 5.054e-01
706.1090
705.864
@@ -428,7 +428,7 @@
-0.466
2.195e-02
- 6.797e-01
+ 5.399e-01
802.3780
802.386
@@ -441,7 +441,7 @@
-0.481
2.195e-02
- 7.330e-01
+ 5.838e-01
883.5000
883.165
@@ -451,7 +451,7 @@
-0.484
2.195e-02
- 7.416e-01
+ 5.909e-01
816.4770
816.485
@@ -464,7 +464,7 @@
-0.500
2.195e-02
- 8.033e-01
+ 6.419e-01
732.8750
732.882
@@ -477,7 +477,7 @@
-0.504
2.195e-02
- 8.198e-01
+ 6.556e-01
717.9330
717.940
@@ -488,7 +488,7 @@
-0.516
2.195e-02
- 8.708e-01
+ 6.979e-01
645.3610
645.367
@@ -498,7 +498,7 @@
-0.518
2.195e-02
- 8.780e-01
+ 7.039e-01
772.4510
772.458
@@ -509,7 +509,7 @@
-0.535
4.159e-02
- 9.510e-01
+ 7.647e-01
1257.4800
1257.670
@@ -521,7 +521,7 @@
-0.536
4.159e-02
- 9.556e-01
+ 7.685e-01
651.8770
651.883
@@ -531,7 +531,7 @@
-0.540
4.159e-02
- 9.785e-01
+ 7.876e-01
798.4490
798.456
@@ -544,7 +544,7 @@
-0.543
5.044e-02
- 9.930e-01
+ 7.997e-01
1374.8800
1375.040
@@ -555,7 +555,7 @@
-0.546
5.044e-02
- 1.000e+00
+ 8.087e-01
628.3770
628.382
@@ -571,7 +571,7 @@
-0.569
5.044e-02
- 1.000e+00
+ 9.088e-01
1223.1100
1223.610
@@ -581,7 +581,7 @@
-0.584
5.044e-02
- 1.000e+00
+ 9.756e-01
492.6210
492.626
@@ -25618,7 +25618,7 @@
0.000000
2.238067e-02
- 5.816870e-02
+ 5.510359e-02
1111.0600
1111.070
ENSP00000295834.3
@@ -25631,7 +25631,7 @@
0.000
2.238e-02
- 5.817e-02
+ 5.510e-02
573.8040
573.810
ENSP00000322421.5
@@ -25646,7 +25646,7 @@
0.000
2.238e-02
- 5.817e-02
+ 5.510e-02
804.7940
804.802
ENSP00000349960.4
@@ -25672,7 +25672,7 @@
-0.017
2.238e-02
- 6.349e-02
+ 5.995e-02
1020.5000
1020.180
ENSP00000378484.3
@@ -25686,7 +25686,7 @@
-0.023
2.238e-02
- 6.553e-02
+ 6.180e-02
568.2950
568.100
ENSP00000237014.3
@@ -25699,7 +25699,7 @@
-0.230
2.238e-02
- 1.945e-01
+ 1.761e-01
538.5580
538.563
ENSP00000482538.1
@@ -25735,7 +25735,7 @@
-0.234
2.238e-02
- 1.983e-01
+ 1.794e-01
700.0860
700.093
ENSP00000295897.4
@@ -25754,7 +25754,7 @@
-0.236
2.238e-02
- 2.007e-01
+ 1.815e-01
1023.0400
1023.050
ENSP00000246662.4
@@ -25766,7 +25766,7 @@
-0.280
2.238e-02
- 2.518e-01
+ 2.258e-01
973.1370
973.145
ENSP00000295834.3
@@ -25779,7 +25779,7 @@
-0.285
2.238e-02
- 2.594e-01
+ 2.324e-01
1128.0700
1127.580
ENSP00000007699.5
@@ -25796,7 +25796,7 @@
-0.289
2.238e-02
- 2.642e-01
+ 2.365e-01
939.5320
939.540
ENSP00000447278.1
@@ -25810,7 +25810,7 @@
-0.289
2.238e-02
- 2.645e-01
+ 2.368e-01
897.9910
898.000
ENSP00000447566.1
@@ -25826,7 +25826,7 @@
-0.324
2.238e-02
- 3.174e-01
+ 2.822e-01
719.1310
719.138
ENSP00000390299.1
@@ -25858,7 +25858,7 @@
-0.329
2.238e-02
- 3.262e-01
+ 2.897e-01
525.2790
525.284
ENSP00000447566.1
@@ -25873,7 +25873,7 @@
-0.342
2.238e-02
- 3.482e-01
+ 3.085e-01
1086.5600
1086.570
ENSP00000357535.3
@@ -25885,7 +25885,7 @@
-0.344
2.238e-02
- 3.522e-01
+ 3.119e-01
831.1240
831.132
ENSP00000234590.4
@@ -25897,7 +25897,7 @@
-0.351
2.238e-02
- 3.661e-01
+ 3.238e-01
863.0590
862.732
ENSP00000000412.3
@@ -25911,7 +25911,7 @@
-0.354
2.238e-02
- 3.717e-01
+ 3.286e-01
876.4500
876.456
ENSP00000447278.1
@@ -25925,7 +25925,7 @@
-0.357
2.238e-02
- 3.761e-01
+ 3.323e-01
1094.5500
1094.560
ENSP00000357535.3
@@ -25937,7 +25937,7 @@
-0.377
2.238e-02
- 4.172e-01
+ 3.672e-01
950.4940
950.502
ENSP00000457733.1
@@ -25951,7 +25951,7 @@
-0.380
2.238e-02
- 4.245e-01
+ 3.733e-01
736.4180
736.425
ENSP00000297185.3
@@ -25963,7 +25963,7 @@
-0.382
2.238e-02
- 4.302e-01
+ 3.782e-01
526.6090
526.614
ENSP00000216281.7
@@ -25980,7 +25980,7 @@
-0.391
2.238e-02
- 4.494e-01
+ 3.944e-01
855.7670
855.774
ENSP00000377082.4
@@ -26008,7 +26008,7 @@
-0.400
2.238e-02
- 4.722e-01
+ 4.136e-01
967.5510
967.559
ENSP00000252244.3
@@ -26022,7 +26022,7 @@
-0.402
2.238e-02
- 4.771e-01
+ 4.178e-01
837.4880
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diff -r dce55ca21b98 -r 07107a686ce9 test-data/percolatorOut_alloptions.xml
--- a/test-data/percolatorOut_alloptions.xml Fri May 19 09:01:27 2017 -0400
+++ b/test-data/percolatorOut_alloptions.xml Thu Aug 13 03:53:33 2020 -0400
@@ -4,15216 +4,56 @@
xmlns:p="http://per-colator.com/percolator_out/15"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://per-colator.com/percolator_out/15 https://github.com/percolator/percolator/raw/pout-1-5/src/xml/percolator_out.xsd"
-p:majorVersion="3" p:minorVersion="01" p:percolator_version="Percolator version 3.01">
+p:majorVersion="3" p:minorVersion="05" p:percolator_version="Percolator version 3.05.0">
- percolator -X percotest -j percolatorTab -Y -p 0.00001 -n 0.00001 -t 0.1 -F 0.1 -i 5 -S 2 -V RawScore -x -u -O -U --decoy-xml-output
+ percolator -j percolatorTab -X percotest --decoy-xml-output -Y -p 1e-05 -n 1e-05 -t 0.1 -F 0.1 -i 5 -S 2 -V RawScore -x -u -O -U
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