| Previous changeset 5:dce55ca21b98 (2017-05-19) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit de8cdf895c3c6113f301a119788701b2465a1b1b" |
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modified:
nested_collection.py nested_collection.xml percolator.xml percolator_converters.xml test-data/empty_file1.mzid test-data/empty_file10.mzid test-data/empty_file11.mzid test-data/empty_file12.mzid test-data/empty_file13.mzid test-data/empty_file14.mzid test-data/empty_file2.mzid test-data/empty_file3.mzid test-data/empty_file4.mzid test-data/empty_file5.mzid test-data/empty_file6.mzid test-data/empty_file7.mzid test-data/empty_file8.mzid test-data/empty_file9.mzid test-data/percolatorInresult.txt test-data/percolatorInresult_multifractions.txt test-data/percolatorOut.xml test-data/percolatorOut_alloptions.xml |
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added:
percolator_macros.xml |
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| 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 |
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| @@ -57,5 +57,6 @@ print('producing', dsetname) os.symlink(args.galaxyfiles[fnindex], dsetname) + if __name__ == '__main__': main() |
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| 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 |
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| @@ -82,7 +82,7 @@ <element name="inputfn07_fraction_eight_spectra" ftype="mzid" file="empty_file8.mzid"/> <element name="inputfn08_fraction_nine_spectra" ftype="mzid" file="empty_file9.mzid"/> <element name="inputfn09_fraction_ten_spectra" ftype="mzid" file="empty_file10.mzid"/> - <element name="inputfn10_fraction_eleven_spectra" ftype="mzid" file="empty_file10.mzid"/> + <element name="inputfn10_fraction_eleven_spectra" ftype="mzid" file="empty_file11.mzid"/> </element> </output_collection> </test> |
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| 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 |
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| @@ -1,8 +1,9 @@ -<tool id="percolator" name="Percolator" version="3.1.0"> +<tool id="percolator" name="Percolator" version="@TOOL_VERSION@+galaxy0"> <description>accurate peptide identification</description> - <requirements> - <requirement type="package" version="3.1">percolator</requirement> - </requirements> + <macros> + <import>percolator_macros.xml</import> + </macros> + <expand macro="requirements" /> <stdio> <exit_code range="1:"/> </stdio> |
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| 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 |
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| @@ -1,8 +1,9 @@ -<tool id="percolator_input_converters" name="Search engine output to Pin converter" version="3.1"> +<tool id="percolator_input_converters" name="Search engine output to Pin converter" version="@TOOL_VERSION@+galaxy0"> <description>to create Percolator input files</description> - <requirements> - <requirement type="package" version="3.1">percolator</requirement> - </requirements> + <macros> + <import>percolator_macros.xml</import> + </macros> + <expand macro="requirements" /> <stdio> <exit_code range="1:"/> </stdio> |
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| 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 |
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| @@ -0,0 +1,9 @@ +<macros> + <token name="@TOOL_VERSION@">3.5</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">percolator</requirement> + <yield/> + </requirements> + </xml> +</macros> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file1.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file10.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file11.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file12.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file13.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file14.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file2.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file3.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file4.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file5.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file6.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file7.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file8.mzid --> |
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| 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 |
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| @@ -0,0 +1,1 @@ +<!-- empty_file9.mzid --> |
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| 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 |
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| 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 |
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| 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 |
| [ |
| b'@@ -4,10 +4,10 @@\n xmlns:p="http://per-colator.com/percolator_out/15" \n xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" \n xsi:schemaLocation="http://per-colator.com/percolator_out/15 https://github.com/percolator/percolator/raw/pout-1-5/src/xml/percolator_out.xsd" \n-p:majorVersion="3" p:minorVersion="01" p:percolator_version="Percolator version 3.01">\n+p:majorVersion="3" p:minorVersion="05" p:percolator_version="Percolator version 3.05.0">\n \n <process_info>\n- <command_line>percolator -X percotest -j percolatorTab --decoy-xml-output</command_line>\n+ <command_line>percolator -j percolatorTab -X percotest --decoy-xml-output -y</command_line>\n <other_command_line></other_command_line>\n <pi_0_psms>0.790264</pi_0_psms>\n <pi_0_peptides>0.805704</pi_0_peptides>\n@@ -19,7 +19,7 @@\n <psm p:psm_id="dataset_2_SII_438_1_9937_2_1" p:decoy="false">\n <svm_score>0.000000</svm_score>\n <q_value>2.195178e-02</q_value>\n- <pep>6.523451e-02</pep>\n+ <pep>4.817157e-02</pep>\n <exp_mass>1111.0600</exp_mass>\n <calc_mass>1111.070</calc_mass>\n <peptide_seq n="K" c="A" seq="[UNIMOD:737]YQLQSQENFEAFMK[UNIMOD:737]"/>\n@@ -30,7 +30,7 @@\n <psm p:psm_id="dataset_3_SII_386_1_9885_4_1" p:decoy="false">\n <svm_score>0.000</svm_score>\n <q_value>2.195e-02</q_value>\n- <pep>6.523e-02</pep>\n+ <pep>4.817e-02</pep>\n <exp_mass>573.8040</exp_mass>\n <calc_mass>573.810</calc_mass>\n <peptide_seq n="K" c="G" seq="[UNIMOD:737]TYFPHFDLSHGSAQVK[UNIMOD:737]"/>\n@@ -43,7 +43,7 @@\n <psm p:psm_id="dataset_3_SII_343_1_9842_3_1" p:decoy="false">\n <svm_score>0.000</svm_score>\n <q_value>2.195e-02</q_value>\n- <pep>6.523e-02</pep>\n+ <pep>4.817e-02</pep>\n <exp_mass>804.7940</exp_mass>\n <calc_mass>804.802</calc_mass>\n <peptide_seq n="R" c="A" seq="[UNIMOD:737]VAPEEHPVLLTEAPLNPK[UNIMOD:737]"/>\n@@ -67,7 +67,7 @@\n <psm p:psm_id="dataset_2_SII_259_1_9758_3_1" p:decoy="false">\n <svm_score>-0.017</svm_score>\n <q_value>2.195e-02</q_value>\n- <pep>7.098e-02</pep>\n+ <pep>5.255e-02</pep>\n <exp_mass>1020.5000</exp_mass>\n <calc_mass>1020.180</calc_mass>\n <peptide_seq n="K" c="V" seq="[UNIMOD:737]TDEFQLHTNVNDGTEFGGSIYQK[UNIMOD:737]"/>\n@@ -79,7 +79,7 @@\n <psm p:psm_id="dataset_3_SII_398_1_9897_5_1" p:decoy="false">\n <svm_score>-0.023</svm_score>\n <q_value>2.195e-02</q_value>\n- <pep>7.318e-02</pep>\n+ <pep>5.422e-02</pep>\n <exp_mass>568.2950</exp_mass>\n <calc_mass>568.100</calc_mass>\n <peptide_seq n="K" c="Y" seq="[UNIMOD:737]ALGISPFHEHAEVVFTANDSGPRR"/>\n@@ -90,7 +90,7 @@\n <psm p:psm_id="dataset_3_SII_306_1_9805_4_1" p:decoy="false">\n <svm_score>-0.230</svm_score>\n <q_value>2.195e-02</q_value>\n- <pep>2.088e-01</pep>\n+ <pep>1.597e-01</pep>\n <exp_mass>538.5580</exp_mass>\n <calc_mass>538.563</calc_mass>\n <peptide_seq n="R" c="L" seq="[UNIMOD:737]HLQLAIRNDEELNK[UNIMOD:737]"/>\n@@ -124,7 +124,7 @@\n <psm p:psm_id="dataset_2_SII_247_1_9746_3_1" p:decoy="false">\n <svm_score>-0.234</svm_score>\n <q_value>2.195e-02</q_value>\n- <pep>2.127e-01</pep>\n+ <pep>1.628e-01</pep>\n <exp_mass>700.0860</exp_mass>\n <calc_mass>700.093</calc_mass>\n <peptide_seq n="K" c="N" seq="[UNIMOD:737]K[UNIMOD:737]VPQVSTPTLVEVSR"/>\n@@ -141,7 +141,7 @@\n <psm p:psm_id="dataset_3_SII_176_1_9675_2_1" p:decoy="false">\n <svm_score>-0.236</svm_score>\n <q_value>2.195e-02</q_value>\n- <pep>2.152e-01</pep>\n+ <pep>1.648e-01</pep>\n <exp_mass>1023.0400</exp_mass>\n <calc_mass>1023.050</calc_mass>\n <peptide_seq n="K" c="I" seq="[UNIMOD:737]VQALEEANNDLENK[UNIMOD:737]"/>\n@@ -151,7 +151,7 @@\n <psm p:psm_id="dataset_3_SII_301_1_9800_3_1" p:decoy="false">\n <svm_score>-0.280</svm_score>\n <q_value>2.195e-02</q_value>\n- <pep>2.678e-01</pep>\n+ <pep>2.065e-01</pep>\n <exp_mass'..b'ein_id>ENSP00000447566.1</protein_id>\n@@ -26127,7 +26127,7 @@\n <peptide p:peptide_id="[UNIMOD:737]SLEDQVEM[UNIMOD:35]LR" p:decoy="false">\n <svm_score>-0.500</svm_score>\n <q_value>2.238e-02</q_value>\n- <pep>7.876e-01</pep>\n+ <pep>6.768e-01</pep>\n <exp_mass>732.8750</exp_mass>\n <calc_mass>732.882</calc_mass>\n <protein_id>ENSP00000465489.1</protein_id>\n@@ -26142,7 +26142,7 @@\n <peptide p:peptide_id="[UNIMOD:737]QIFLGGVDK[UNIMOD:737]" p:decoy="false">\n <svm_score>-0.504</svm_score>\n <q_value>2.238e-02</q_value>\n- <pep>8.044e-01</pep>\n+ <pep>6.907e-01</pep>\n <exp_mass>717.9330</exp_mass>\n <calc_mass>717.940</calc_mass>\n <protein_id>ENSP00000360671.4</protein_id>\n@@ -26155,7 +26155,7 @@\n <peptide p:peptide_id="[UNIMOD:737]TLLDIDNTR" p:decoy="false">\n <svm_score>-0.516</svm_score>\n <q_value>2.238e-02</q_value>\n- <pep>8.564e-01</pep>\n+ <pep>7.336e-01</pep>\n <exp_mass>645.3610</exp_mass>\n <calc_mass>645.367</calc_mass>\n <protein_id>ENSP00000246662.4</protein_id>\n@@ -26167,7 +26167,7 @@\n <peptide p:peptide_id="[UNIMOD:737]LSLNIDPDAK[UNIMOD:737]" p:decoy="false">\n <svm_score>-0.518</svm_score>\n <q_value>2.238e-02</q_value>\n- <pep>8.637e-01</pep>\n+ <pep>7.397e-01</pep>\n <exp_mass>772.4510</exp_mass>\n <calc_mass>772.458</calc_mass>\n <protein_id>ENSP00000299767.4</protein_id>\n@@ -26180,7 +26180,7 @@\n <peptide p:peptide_id="[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]EK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]HK[UNIMOD:737]K[UNIMOD:737]HK[UNIMOD:737]K[UNIMOD:737]HK[UNIMOD:737]K[UNIMOD:737]HK[UNIMOD:737]" p:decoy="true">\n <svm_score>-0.535</svm_score>\n <q_value>4.241e-02</q_value>\n- <pep>9.383e-01</pep>\n+ <pep>8.011e-01</pep>\n <exp_mass>1257.4800</exp_mass>\n <calc_mass>1257.670</calc_mass>\n <protein_id>decoy_ENSP00000317872.4</protein_id>\n@@ -26194,7 +26194,7 @@\n <peptide p:peptide_id="[UNIMOD:737]ILGATIENSR" p:decoy="false">\n <svm_score>-0.536</svm_score>\n <q_value>4.241e-02</q_value>\n- <pep>9.429e-01</pep>\n+ <pep>8.049e-01</pep>\n <exp_mass>651.8770</exp_mass>\n <calc_mass>651.883</calc_mass>\n <protein_id>ENSP00000355124.3</protein_id>\n@@ -26206,7 +26206,7 @@\n <peptide p:peptide_id="[UNIMOD:737]YEELQSLAGK[UNIMOD:737]" p:decoy="false">\n <svm_score>-0.540</svm_score>\n <q_value>4.241e-02</q_value>\n- <pep>9.664e-01</pep>\n+ <pep>8.242e-01</pep>\n <exp_mass>798.4490</exp_mass>\n <calc_mass>798.456</calc_mass>\n <protein_id>ENSP00000447566.1</protein_id>\n@@ -26221,7 +26221,7 @@\n <peptide p:peptide_id="[UNIMOD:737]EK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]MK[UNIMOD:737]DANENK[UNIMOD:737]LLK[UNIMOD:737]ESK[UNIMOD:737]MQK[UNIMOD:737]K[UNIMOD:737]ESK[UNIMOD:737]K[UNIMOD:737]SK[UNIMOD:737]EQK[UNIMOD:737]EK[UNIMOD:737]SK[UNIMOD:737]" p:decoy="true">\n <svm_score>-0.543</svm_score>\n <q_value>5.143e-02</q_value>\n- <pep>9.812e-01</pep>\n+ <pep>8.364e-01</pep>\n <exp_mass>1374.8800</exp_mass>\n <calc_mass>1375.040</calc_mass>\n <protein_id>decoy_ENSP00000206423.3</protein_id>\n@@ -26234,7 +26234,7 @@\n <peptide p:peptide_id="[UNIMOD:737]AVDSLVPIGR" p:decoy="false">\n <svm_score>-0.546</svm_score>\n <q_value>5.143e-02</q_value>\n- <pep>9.922e-01</pep>\n+ <pep>8.454e-01</pep>\n <exp_mass>628.3770</exp_mass>\n <calc_mass>628.382</calc_mass>\n <protein_id>ENSP00000465477.2</protein_id>\n@@ -26252,7 +26252,7 @@\n <peptide p:peptide_id="[UNIMOD:737]DLYANTVLSGGSTM[UNIMOD:35]YPGIADR" p:decoy="false">\n <svm_score>-0.569</svm_score>\n <q_value>5.143e-02</q_value>\n- <pep>1.000e+00</pep>\n+ <pep>9.457e-01</pep>\n <exp_mass>1223.1100</exp_mass>\n <calc_mass>1223.610</calc_mass>\n <protein_id>ENSP00000416706.1</protein_id>\n' |
| b |
| 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 |
| [ |
| b'@@ -4,15216 +4,56 @@\n xmlns:p="http://per-colator.com/percolator_out/15" \n xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" \n xsi:schemaLocation="http://per-colator.com/percolator_out/15 https://github.com/percolator/percolator/raw/pout-1-5/src/xml/percolator_out.xsd" \n-p:majorVersion="3" p:minorVersion="01" p:percolator_version="Percolator version 3.01">\n+p:majorVersion="3" p:minorVersion="05" p:percolator_version="Percolator version 3.05.0">\n \n <process_info>\n- <command_line>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</command_line>\n+ <command_line>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</command_line>\n <other_command_line></other_command_line>\n <pi_0_psms>1</pi_0_psms>\n <psms_qlevel>0</psms_qlevel>\n </process_info>\n \n <psms>\n- <psm p:psm_id="dataset_3_SII_77_1_9576_2_1" p:decoy="false">\n- <svm_score>0.000000</svm_score>\n- <q_value>1.000000e+00</q_value>\n- <pep>1.000000e+00</pep>\n- <exp_mass>419.7500</exp_mass>\n- <calc_mass>420.250</calc_mass>\n- <peptide_seq n="R" c="P" seq="[UNIMOD:737]PPPGSR"/>\n- <protein_id>ENSP00000361434.5</protein_id>\n- <protein_id>ENSP00000436727.1</protein_id>\n- <protein_id>ENSP00000361429.3</protein_id>\n- <protein_id>ENSP00000391998.3</protein_id>\n- <protein_id>ENSP00000387435.3</protein_id>\n- <p_value>0.000e+00</p_value>\n- </psm>\n- <psm p:psm_id="dataset_88023_SII_9148_1_9148_2_1" p:decoy="true">\n- <svm_score>0.000</svm_score>\n- <q_value>1.000e+00</q_value>\n- <pep>1.000e+00</pep>\n- <exp_mass>401.7190</exp_mass>\n- <calc_mass>402.223</calc_mass>\n- <peptide_seq n="K" c="P" seq="[UNIMOD:737]PGMGGR"/>\n- <protein_id>decoy_ENSP00000412580.2</protein_id>\n- <protein_id>decoy_ENSP00000347042.5</protein_id>\n- <protein_id>decoy_ENSP00000346437.3</protein_id>\n- <p_value>0.000e+00</p_value>\n- </psm>\n- <psm p:psm_id="dataset_88023_SII_6492_1_6492_2_1" p:decoy="true">\n- <svm_score>0.000</svm_score>\n- <q_value>1.000e+00</q_value>\n- <pep>1.000e+00</pep>\n- <exp_mass>474.7240</exp_mass>\n- <calc_mass>475.225</calc_mass>\n- <peptide_seq n="R" c="-" seq="[UNIMOD:737]PVC[UNIMOD:4]C[UNIMOD:4]QG"/>\n- <protein_id>decoy_ENSP00000357675.1</protein_id>\n- <p_value>0.000e+00</p_value>\n- </psm>\n- <psm p:psm_id="dataset_2_SII_492_1_9991_5_1" p:decoy="false">\n- <svm_score>-0.017</svm_score>\n- <q_value>1.000e+00</q_value>\n- <pep>1.000e+00</pep>\n- <exp_mass>900.4430</exp_mass>\n- <calc_mass>900.646</calc_mass>\n- <peptide_seq n="R" c="S" seq="[UNIMOD:737]PRLK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]RK[UNIMOD:737]K[UNIMOD:737]R"/>\n- <protein_id>ENSP00000485049.1</protein_id>\n- <p_value>0.000e+00</p_value>\n- </psm>\n- <psm p:psm_id="dataset_88023_SII_9938_1_9938_3_1" p:decoy="true">\n- <svm_score>-0.056</svm_score>\n- <q_value>1.000e+00</q_value>\n- <pep>1.000e+00</pep>\n- <exp_mass>342.8710</exp_mass>\n- <calc_mass>343.206</calc_mass>\n- <peptide_seq n="R" c="P" seq="[UNIMOD:737]LRC[UNIMOD:4]PPR"/>\n- <protein_id>decoy_ENSP00000263408.4</protein_id>\n- <p_value>0.000e+00</p_value>\n- </psm>\n- <psm p:psm_id="dataset_88023_SII_9732_1_9732_3_1" p:decoy="true">\n- <svm_score>-0.073</svm_score>\n- <q_value>1.000e+00</q_value>\n- <pep>1.000e+00</pep>\n- <exp_mass>304.8620</exp_mass>\n- <calc_mass>305.194</calc_mass>\n- <peptide_seq n="R" c="P" seq="[UNIMOD:737]DALPLR"/>\n- <protein_id>decoy_ENSP00000400713.2</protein_id>\n- <p_value>0.000e+00</p_value>\n- </psm>\n- <psm p:psm_id="dataset_88023_SII_9301_1_9301_2_1" p:decoy="true">\n- <svm_score>-0.113</svm_score>\n- <q_value>1.000e+00</q_v'..b'</exp_mass>\n+ <calc_mass>696.262</calc_mass>\n+ <peptide_seq n="K" c="-" seq="[UNIMOD:737]DSSDDDDDDDSMDNLPS"/>\n+ <protein_id>decoy_ENSP00000322373.3</protein_id>\n+ <protein_id>decoy_ENSP00000427792.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_6830_1_6830_2_1" p:decoy="true">\n+ <svm_score>-1.704</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>405.6980</exp_mass>\n+ <calc_mass>405.697</calc_mass>\n+ <peptide_seq n="K" c="-" seq="[UNIMOD:737]GASSEM"/>\n+ <protein_id>decoy_ENSP00000387702.2</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_7099_1_7099_2_1" p:decoy="true">\n+ <svm_score>-1.723</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>437.2190</exp_mass>\n+ <calc_mass>437.718</calc_mass>\n+ <peptide_seq n="R" c="-" seq="[UNIMOD:737]GDSVHM"/>\n+ <protein_id>decoy_ENSP00000349803.3</protein_id>\n+ <protein_id>decoy_ENSP00000420324.1</protein_id>\n+ <protein_id>decoy_ENSP00000418092.1</protein_id>\n+ <protein_id>decoy_ENSP00000419902.1</protein_id>\n+ <protein_id>decoy_ENSP00000419153.1</protein_id>\n+ <protein_id>decoy_ENSP00000417307.1</protein_id>\n+ <protein_id>decoy_ENSP00000377375.2</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_5658_1_5658_2_1" p:decoy="true">\n+ <svm_score>-1.728</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>398.6900</exp_mass>\n+ <calc_mass>397.687</calc_mass>\n+ <peptide_seq n="K" c="-" seq="[UNIMOD:737]GSGC[UNIMOD:4]AN"/>\n+ <protein_id>decoy_ENSP00000434438.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_6150_1_6150_2_1" p:decoy="true">\n+ <svm_score>-1.738</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>405.6980</exp_mass>\n+ <calc_mass>405.196</calc_mass>\n+ <peptide_seq n="K" c="-" seq="[UNIMOD:737]GVC[UNIMOD:4]MGG"/>\n+ <protein_id>decoy_ENSP00000421279.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_5487_1_5487_2_1" p:decoy="true">\n+ <svm_score>-1.765</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>426.7030</exp_mass>\n+ <calc_mass>426.699</calc_mass>\n+ <peptide_seq n="K" c="-" seq="[UNIMOD:737]AC[UNIMOD:4]NGMA"/>\n+ <protein_id>decoy_ENSP00000427514.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_6279_1_6279_2_1" p:decoy="true">\n+ <svm_score>-1.782</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>428.6990</exp_mass>\n+ <calc_mass>427.692</calc_mass>\n+ <peptide_seq n="K" c="-" seq="[UNIMOD:737]DDATM[UNIMOD:35]G"/>\n+ <protein_id>decoy_ENSP00000316809.7</protein_id>\n+ <protein_id>decoy_ENSP00000441869.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_10067_1_10067_6_1" p:decoy="true">\n+ <svm_score>-1.862</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>854.9230</exp_mass>\n+ <calc_mass>854.916</calc_mass>\n+ <peptide_seq n="K" c="D" seq="[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]DK[UNIMOD:737]EK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]EEK[UNIMOD:737]SK[UNIMOD:737]"/>\n+ <protein_id>decoy_ENSP00000384264.3</protein_id>\n+ <protein_id>decoy_ENSP00000426862.1</protein_id>\n+ <protein_id>decoy_ENSP00000389881.2</protein_id>\n+ <protein_id>decoy_ENSP00000443401.2</protein_id>\n+ <protein_id>decoy_ENSP00000351320.4</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n </psms>\n \n </percolator_output>\n' |