| Previous changeset 1:528bcf03e561 (2020-07-17) Next changeset 3:962599ac5406 (2022-01-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407" |
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modified:
macros.xml pepquery.xml test-data/novel_peptides |
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added:
test-data/immunopeptidomics.mgf test-data/pFind.qry.res test-data/test.tags |
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| diff -r 528bcf03e561 -r 5b5a9f59e2c7 macros.xml --- a/macros.xml Fri Jul 17 17:05:41 2020 -0400 +++ b/macros.xml Mon Mar 15 12:52:03 2021 +0000 |
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| @@ -1,5 +1,6 @@ <macros> - <token name="@VERSION@">1.6.0</token> + <token name="@TOOL_VERSION@">1.6.2</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="modifications"> <option value="1">HexNAc of T (203.07937251951) modaa</option> <option value="2">HexNAc of S (203.07937251951) modaa</option> |
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| diff -r 528bcf03e561 -r 5b5a9f59e2c7 pepquery.xml --- a/pepquery.xml Fri Jul 17 17:05:41 2020 -0400 +++ b/pepquery.xml Mon Mar 15 12:52:03 2021 +0000 |
| [ |
| b'@@ -1,10 +1,10 @@\n-<tool id="pepquery" name="PepQuery" version="@VERSION@.0">\n+<tool id="pepquery" name="PepQuery" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n <description>Peptide-centric search engine for novel peptide identification and validation.</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <requirements> \n- <requirement type="package" version="@VERSION@">pepquery</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>\n </requirements>\n <stdio>\n <exit_code range="1:" level="fatal" description="Failed" />\n@@ -19,6 +19,9 @@\n #set $db_file = $re.sub(\'\\s\',\'_\',$re.sub(\'[.][^.]*$\',\'\',$req_inputs.db_file.display_name.split(\'/\')[-1])) + ".fa"\n ln -s \'$req_inputs.spectrum_file\' \'$spectrum_file\' &&\n ln -s \'$req_inputs.db_file\' \'$db_file\' &&\n+ #if $req_inputs.tags.tagType == \'pFind\':\n+ pepquery main.java.util.generateTags \'$req_inputs.tags.qry_res\' > qry.tags &&\n+ #end if\n pepquery \n -ms \'$spectrum_file\'\n -db \'$db_file\'\n@@ -42,6 +45,13 @@\n #end if\n #end if\n -indexType $req_inputs.indexType\n+ #if $req_inputs.tags.tagType == \'PepQuery\':\n+ -tag \'$req_inputs.tags.tag_file\'\n+ -tagIndexType $req_inputs.tags.tagIndexType\n+ #elif $req_inputs.tags.tagType == \'pFind\':\n+ -tag qry.tags\n+ -tagIndexType 2\n+ #end if\n #if $modifications.fixed_mod\n -fixMod \'$modifications.fixed_mod\'\n #end if\n@@ -73,11 +83,11 @@\n <inputs>\n <section name="req_inputs" title="Input Data" expanded="true">\n <conditional name="input_type">\n- <param name="input_type_selector" type="select" label="Input Type" argument="-t" help="" >\n+ <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >\n <option value="peptide">peptide</option>\n <option value="1">protein</option>\n <option value="2">DNA (translate to protein sequences)</option>\n- <!-- these are not working with pepquery version 1.3\n+ <!-- these are not working with pepquery version 1.6\n <option value="3">VCF (translate to protein sequences)</option>\n <option value="4">BED (translate to protein sequences)</option>\n <option value="5">GTF (translate to protein sequences)</option>\n@@ -90,10 +100,10 @@\n <option value="single">Single peptide entered as text</option>\n </param> \n <when value="multiple">\n- <param name="input" type="data" format="txt" label="Peptide Sequences (.txt)" argument="-pep" help="Peptide sequence file containing peptides which you want to search (no column header, 1 peptide per line)." />\n+ <param name="input" argument="-pep" type="data" format="txt" label="Peptide Sequences (.txt)" help="Peptide sequence file containing peptides which you want to search (no column header, 1 peptide per line)." />\n </when>\n <when value="single">\n- <param name="input" type="text" label="Peptide Sequence" argument="-pep" help="Peptide sequence which you want to search">\n+ <param name="input" argument="-pep" type="text" label="Peptide Sequence" help="Peptide sequence which you want to search">\n <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>\n </param>\n </when>\n@@ -106,20 +116,20 @@'..b'text="controllerType=0 controllerNumber=1 scan=19905" />\n+ </assert_contents>\n+ </output>\n+ <output name="query_tags" file="test.tags"/>\n+ <!--\n+ -->\n+ </test>\n+\n </tests>\n <help><![CDATA[\n-PepQuery is a peptide-centric search engine for novel peptide identification and validation. Cancer genomics studies have identified a large number of genomic alterations that may lead to novel, cancer-specific protein sequences. Proteins resulted from these genomic alterations are attractive candidates for cancer biomarkers and therapeutic targets. The leading approach to proteomic validation of genomic alterations is to analyze tandem mass spectrometry (MS/MS) data using customized proteomics databases created from genomics data. Such analysis is time-consuming and requires thorough training and detailed knowledge in proteomics data analysis, leading to a gap between MS/MS data and the cancer genomics community. PepQuery does not require customized databases and allows quick and easy proteomic validation of genomic alterations.\n+**PepQuery**\n+\n+PepQuery_ is a peptide-centric search engine for novel peptide identification and validation. Cancer genomics studies have identified a large number of genomic alterations that may lead to novel, cancer-specific protein sequences. Proteins resulted from these genomic alterations are attractive candidates for cancer biomarkers and therapeutic targets. The leading approach to proteomic validation of genomic alterations is to analyze tandem mass spectrometry (MS/MS) data using customized proteomics databases created from genomics data. Such analysis is time-consuming and requires thorough training and detailed knowledge in proteomics data analysis, leading to a gap between MS/MS data and the cancer genomics community. PepQuery does not require customized databases and allows quick and easy proteomic validation of genomic alterations.\n \n **Inputs**\n - A sequence to match, one of the following:\n@@ -438,24 +648,38 @@\n \n - A mass spectrometry MGF file \n - A reference protein fasta database, peptides matching a reference sequence will be excluded. \n+ - An optional tags file for no-enzyme immunopeptidomics search \n+\n+ - See: http://pepquery.org/data/PepQuery_for_immunopeptidomics_data.pdf\n \n **Outputs**\n - PSM annotation - tabular with columns: \n- peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity\n+ \n+ - peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity\n+\n - Detail - tabular with columns: \n- *report_spectrum_file* spectrum_title peptide modification pep_mass score\n+ \n+ - *report_spectrum_file* spectrum_title peptide modification pep_mass score\n+\n - PSM - tabular with columns: \n- peptide modification n *report_spectrum_file* spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue\n+ \n+ - peptide modification n *report_spectrum_file* spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue\n+\n - PSM Rank - tabular with columns: \n- peptide modification n *report_spectrum_file* spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank *n_ptm*\n+ \n+ - peptide modification n *report_spectrum_file* spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank *n_ptm*\n+\n - An MGF with the best matching spectrums\n \n The *report_spectrum_file* is an optional field that can be added. \n+\n The *n_ptm* field is added when using unrestricted modification searching (-um).\n \n+.. _PepQuery: http://pepquery.org/document.html\n \n ]]></help>\n <citations>\n <citation type="doi">10.1101/gr.235028.118</citation>\n+ <citation type="doi">10.1038/s41467-020-15456-w</citation>\n </citations>\n </tool>\n' |
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| diff -r 528bcf03e561 -r 5b5a9f59e2c7 test-data/immunopeptidomics.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/immunopeptidomics.mgf Mon Mar 15 12:52:03 2021 +0000 |
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| b'@@ -0,0 +1,464 @@\n+BEGIN IONS\n+TITLE=controllerType=0 controllerNumber=1 scan=19846\n+RTINSECONDS=2320.06458\n+PEPMASS=383.529876708984\n+CHARGE=3+\n+84.0449677 46347.0703125\n+84.0813446 85493.9453125\n+86.0719299 7175.7060546875\n+86.0969772 135316.21875\n+87.0795746 57686.53515625\n+89.5852509 6013.955078125\n+91.0547638 26870.0390625\n+100.0871506 10508.3408203125\n+101.0712357 8028.2236328125\n+102.0548477 7109.3364257813\n+110.071434 72448.5390625\n+112.0872192 68537.90625\n+116.0708847 66026.75\n+116.6829987 7043.2426757813\n+119.0492325 28436.21484375\n+120.0808487 28182.986328125\n+123.0442657 6282.2768554688\n+127.0979004 32528.88671875\n+129.1026154 74929.3046875\n+129.1124268 15517.341796875\n+132.1023407 7616.8291015625\n+136.075592 267654.46875\n+137.0793915 44604.71484375\n+140.0816498 8406.1591796875\n+145.4732819 7887.0209960938\n+147.0440521 10594.44921875\n+147.1123962 10032.357421875\n+155.0816803 6984.1274414063\n+157.1085968 34948.90234375\n+165.0540466 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5714.333984375\n+755.3690186 3943.5083007813\n+764.3662109 6421.2250976563\n+772.3707886 3762.69140625\n+789.3843384 4607.880859375\n+791.3812256 3588.5078125\n+798.3960571 6360.8334960938\n+806.4115601 30085.07421875\n+832.4921875 4568.6284179688\n+833.508728 4909.1865234375\n+860.4714355 13005.275390625\n+895.4536743 16561.779296875\n+896.4584961 4322.0971679688\n+END IONS\n' |
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| diff -r 528bcf03e561 -r 5b5a9f59e2c7 test-data/novel_peptides --- a/test-data/novel_peptides Fri Jul 17 17:05:41 2020 -0400 +++ b/test-data/novel_peptides Mon Mar 15 12:52:03 2021 +0000 |
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| @@ -1,3 +1,6 @@ DSGASGSILEASAAR ELGSSDLTAR SPYREFTDHLVK +RQVPEHLGP +RPGPGTRKSL +MTDRHAGTY |
| b |
| diff -r 528bcf03e561 -r 5b5a9f59e2c7 test-data/pFind.qry.res --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pFind.qry.res Mon Mar 15 12:52:03 2021 +0000 |
| [ |
| @@ -0,0 +1,32 @@ +S 1148.575077 3 +controllerType=0 controllerNumber=1 scan=19846 +1 FACNGTGGIIVP 1148.576804 3.554176 0.977448 0.268814 0 0 1 0 1 11340;1979;S;V 0 -0.001047 0.000000 5.000000 0.145238 1.000000 18 0 0 0 1344 0 0 0 +2 TLMEQTLPVT 1148.586699 4.380692 0.986473 0.268814 1 3 Oxidation[M]#0 0 0 0 2 32727;102;F;V 93939;102;F;V 0 0.005119 1.000000 2.000000 0.157397 2.000000 109 0 0 0 384 0 0 0 +3 RSDALGGCLSL 1148.572781 3.598858 0.991751 0.268814 1 8 Carbamidomethyl[C]#0 0 1 0 1 5598;401;D;A 0 0.000261 1.000000 6.000000 0.087418 2.000000 1 0 0 0 800 0 0 0 +4 SETLSIVCPSI 1148.586698 4.274827 0.995714 0.268814 0 0 0 0 1 120267;1812;Q;I 0 0.000569 1.000000 4.000000 0.131591 2.000000 648 0 0 0 800 0 0 0 +5 RPSTASGSSVVT 1148.590536 3.900134 0.995843 0.268814 0 0 0 0 1 33405;1207;H;A 0 0.001153 1.000000 6.000000 0.155589 2.000000 3 0 0 0 1568 0 0 0 +6 FGQVAASTAPSL 1148.594562 3.942397 0.997807 0.268814 0 0 0 0 7 18779;1673;V;F 57765;21;V;F 68677;499;V;F 72305;1102;V;F 106433;450;V;F 118259;1661;V;F 149057;526;V;F 0 0.002566 1.000000 7.000000 0.115885 2.000000 1088 0 0 0 1600 0 0 0 +7 QDGPGFKSISL 1148.594562 3.621902 0.997928 0.268814 0 0 1 0 3 25722;229;V;R 46484;120;V;R 119316;229;V;R 0 0.002473 1.000000 6.000000 0.127843 2.000000 512 0 0 0 800 0 0 0 +S 1067.448778 2 +controllerType=0 controllerNumber=1 scan=19905 +1 VDQEGANSMT 1067.430933 3.505104 0.997174 0.444184 1 9 Oxidation[M]#0 0 0 0 3 20025;195;D;A 133965;196;D;A 138831;195;D;A 0 0.006154 1.000000 4.000000 0.098087 2.000000 1 0 0 0 408 0 0 0 +2 FYGNSISIS 1067.444476 3.014719 0.998504 0.444184 1 7 Phospho[S]#0 0 0 0 1 11805;412;S;A 0 0.006294 1.000000 3.000000 0.054075 2.000000 32 0 0 0 70 0 0 0 +3 KDPGMGAMGGM 1067.431801 3.263346 0.998586 0.444184 1 11 Oxidation[M]#0 0 0 0 1 23457;553;E;G 0 -0.000013 1.000000 5.000000 0.087146 2.000000 261 0 0 0 400 0 0 0 +4 FYGNSISIS 1067.444476 3.028426 0.998621 0.444184 1 9 Phospho[S]#0 0 0 0 1 11805;412;S;A 0 0.003416 1.000000 3.000000 0.032929 2.000000 160 0 0 0 134 0 0 0 +S 1142.501268 2 +controllerType=0 controllerNumber=1 scan=19907 +1 MQSSQSMSKL 1142.517968 3.710725 0.978768 0.276033 1 7 Oxidation[M]#0 0 0 0 1 33;841;I;T 0 -0.001474 0.000000 3.000000 0.145364 3.000000 0 0 0 0 302 0 0 0 +2 MQSSQSMSKL 1142.517968 1.886902 0.998416 0.276033 1 1 Oxidation[M]#0 0 0 0 1 33;841;I;T 0 0.003725 0.000000 6.000000 0.104444 1.000000 5 0 0 0 256 0 0 0 +3 DTITQKVEE 1142.497627 1.828102 0.999712 0.276033 1 4 Phospho[T]#0 0 0 0 5 6567;5813;S;I 65345;3767;S;I 73025;5704;S;I 100015;919;S;I 103069;3727;S;I 0 -0.011066 1.000000 5.000000 0.145552 1.000000 130 0 0 0 0 0 0 0 +S 928.482124 2 +controllerType=0 controllerNumber=1 scan=19946 +1 GPRLPGSSSA 928.484626 7.710279 0.421887 0.011383 0 0 0 0 1 26031;290;E;A 0 0.001328 1.000000 0.000000 0.207882 8.000000 510 0 0 0 488 0 0 0 +2 PLGRPGSSGT 928.484626 5.893959 0.818989 0.011383 0 0 1 0 4 23498;63;G;G 50106;66;G;G 69602;63;G;G 147656;118;G;G 0 0.002600 1.000000 1.000000 0.212426 5.000000 250 0 0 0 488 0 0 0 +3 IVNPGRDSA 928.484626 4.782812 0.975088 0.011383 0 0 0 0 8 8187;441;A;T 50181;441;A;T 50183;441;A;T 54737;441;A;T 61191;441;A;T 73135;441;A;T 85927;441;A;T 133089;441;A;T 0 0.000119 1.000000 3.000000 0.149306 3.000000 232 0 0 0 200 0 0 0 +4 PRLPGSSSA 928.484629 8.003373 0.979251 0.011383 1 0 Carbamidomethyl[AnyN-term]#0 0 0 0 1 26031;291;G;A 0 0.001326 1.000000 0.000000 0.207882 8.000000 255 0 0 0 244 0 0 0 +5 GAPLAAPFGGA 928.488651 4.541935 0.980862 0.011383 0 0 1 0 1 7256;3036;P;G 0 0.002595 1.000000 3.000000 0.134447 4.000000 582 0 0 0 960 0 0 0 +6 RKAPDPSGT 928.484626 3.961262 0.983572 0.011383 0 0 0 0 1 26911;595;S;G 0 0.003601 1.000000 3.000000 0.147253 3.000000 99 0 0 0 224 0 0 0 +7 RPVGASPSSA 928.484626 4.484990 0.987448 0.011383 0 0 1 0 1 680;164;A;Q 0 0.000146 1.000000 5.000000 0.155946 3.000000 449 0 0 0 448 0 0 0 +8 HLLFGPSSA 928.488651 4.685283 0.989669 0.011383 0 0 0 0 4 23883;190;Y;L 58837;221;Y;L 77055;191;Y;L 117305;220;Y;L 0 -0.003066 1.000000 4.000000 0.200977 3.000000 225 0 0 0 224 0 0 0 +9 QLQPKSSSA 928.473392 4.929118 0.990178 0.011383 1 0 Gln->pyro-Glu[AnyN-termQ]#0 0 0 0 2 6245;3970;I;G 136775;870;I;G 0 0.007494 1.000000 3.000000 0.156720 4.000000 240 0 0 0 240 0 0 0 +10 NAHISKTSA 928.484626 3.752999 0.992705 0.011383 0 0 1 0 6 25928;751;F;P 42420;742;F;P 47934;768;F;P 58152;692;F;P 101556;692;F;P 141526;759;F;P 0 -0.000622 1.000000 4.000000 0.126520 2.000000 193 0 0 0 208 0 0 0 |
| b |
| diff -r 528bcf03e561 -r 5b5a9f59e2c7 test-data/test.tags --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.tags Mon Mar 15 12:52:03 2021 +0000 |
| b |
| @@ -0,0 +1,3 @@ +controllerType=0 controllerNumber=1 scan=19846 FACNGTGGIIVP;TLMEQTLPVT;RSDALGGCLSL;SETLSIVCPSI;RPSTASGSSVVT;FGQVAASTAPSL;QDGPGFKSISL +controllerType=0 controllerNumber=1 scan=19905 VDQEGANSMT;FYGNSISIS;KDPGMGAMGGM;FYGNSISIS +controllerType=0 controllerNumber=1 scan=19907 MQSSQSMSKL;MQSSQSMSKL;DTITQKVEE |