From 8d8a4fe3c27653bc471d1111d1b7244aa44090f8 Mon Sep 17 00:00:00 2001 From: langella <langella@b8ef2a07-7df7-436f-90b9-41648038564b> Date: Tue, 7 Feb 2012 11:05:58 +0000 Subject: [PATCH] new xml schema for XPIP git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@189 b8ef2a07-7df7-436f-90b9-41648038564b --- xtandempipeline/doc/files/xpip/xpip.xsd | 252 ++++++++++++++++++ .../doc/files/xpip/xpip_sample.xml | 62 +++++ 2 files changed, 314 insertions(+) create mode 100644 xtandempipeline/doc/files/xpip/xpip.xsd create mode 100644 xtandempipeline/doc/files/xpip/xpip_sample.xml diff --git a/xtandempipeline/doc/files/xpip/xpip.xsd b/xtandempipeline/doc/files/xpip/xpip.xsd new file mode 100644 index 000000000..a47e7b914 --- /dev/null +++ b/xtandempipeline/doc/files/xpip/xpip.xsd @@ -0,0 +1,252 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!-- XPIP version 1.0 --> +<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"> + <xs:element name="xtandem_pipeline" type="xtandem_pipelineType" /> + <xs:element name="information" type="informationType" /> + <xs:element name="filter_params" type="filter_paramsType" /> + <xs:element name="identifications" type="identificationsType" /> + <xs:element name="identification" type="identificationType" /> + <xs:element name="modifs_list_mass" type="modifs_list_massType" /> + <xs:element name="modifs_mass" type="modifs_massType" /> + <xs:element name="samples" type="samplesType" /> + <xs:element name="sample" type="sampleType" /> + <xs:element name="match_list" type="match_listType" /> + <xs:element name="match" type="matchType" /> + <xs:element name="protein" type="proteinType" /> + <xs:element name="protein_evalue" type="protein_evalueType" /> + <xs:element name="sequence" type="xs:string" /> + + + <!-- <protein_evalue evalue="-5.853872" sample="20110323_Pontlezica_Raphael_1_B06_EFJ2-16.xml" + /> --> + <xs:complexType name="protein_evalueType"> + <xs:annotation> + <xs:documentation> + a protein + </xs:documentation> + </xs:annotation> + <xs:attribute name="evalue" type="xs:float"></xs:attribute> + <xs:attribute name="sample" type="xs:string"></xs:attribute> + </xs:complexType> + + <!-- <protein peptide_number="1972" evalue="-275.23846" URL="contaminants_standarts.fasta" + description="conta|P04264|K2C1_HUMAN Keratin, type II cytoskeletal 1 (Cytokeratin + 1) (K1) (CK 1) (67 kDa cytokeratin) (Hair alpha protein) - Homo sapiens (Human)."> --> + <xs:complexType name="proteinType"> + <xs:annotation> + <xs:documentation> + a protein + </xs:documentation> + </xs:annotation> + <xs:sequence> + <xs:element ref="protein_evalue" maxOccurs="unbounded" + minOccurs="1" /> + <xs:element ref="sequence" maxOccurs="1" minOccurs="0" /> + </xs:sequence> + <xs:attribute name="peptide_number" type="xs:int"> + </xs:attribute> + <xs:attribute name="evalue" type="xs:float"> + </xs:attribute> + <xs:attribute name="URL" type="xs:string"> + </xs:attribute> + <xs:attribute name="description" type="xs:string"> + </xs:attribute> + </xs:complexType> + + <xs:complexType name="matchType"> + <xs:annotation> + <xs:documentation> + a match + </xs:documentation> + </xs:annotation> + <xs:sequence> + <xs:element ref="protein" maxOccurs="1" minOccurs="1" /> + </xs:sequence> + <xs:attribute name="validate" type="xs:boolean"> + </xs:attribute> + </xs:complexType> + + + <xs:complexType name="match_listType"> + <xs:annotation> + <xs:documentation> + list of matches + </xs:documentation> + </xs:annotation> + <xs:sequence> + <xs:element ref="match" maxOccurs="unbounded" minOccurs="0" /> + </xs:sequence> + </xs:complexType> + + + <!-- <sample value="2010_01_19_Pont_Lezica_Rafael_28_1_13_EENA1-13.xml" + /> --> + <xs:complexType name="sampleType"> + <xs:annotation> + <xs:documentation> + sample description + </xs:documentation> + </xs:annotation> + <xs:attribute name="value" type="xs:string" use="required"></xs:attribute> + </xs:complexType> + + <xs:complexType name="samplesType"> + <xs:annotation> + <xs:documentation> + list of samples + </xs:documentation> + </xs:annotation> + <xs:sequence> + <xs:element ref="sample" maxOccurs="unbounded" minOccurs="0" /> + </xs:sequence> + </xs:complexType> + + <!-- <modifs_mass modvalue="-18.0106" /> --> + <xs:complexType name="modifs_massType"> + <xs:annotation> + <xs:documentation> + mass modification + </xs:documentation> + </xs:annotation> + <xs:attribute name="modvalue" type="xs:float" use="required"></xs:attribute> + </xs:complexType> + + + <xs:complexType name="modifs_list_massType"> + <xs:annotation> + <xs:documentation> + list of mass modifications + </xs:documentation> + </xs:annotation> + <xs:sequence> + <xs:element ref="modifs_mass" maxOccurs="unbounded" + minOccurs="0" /> + </xs:sequence> + </xs:complexType> + + <xs:complexType name="identificationType"> + <xs:annotation> + <xs:documentation> + identification + </xs:documentation> + </xs:annotation> + <xs:sequence> + <xs:element ref="modifs_list_mass" maxOccurs="1" + minOccurs="1" /> + <xs:element ref="samples" maxOccurs="1" minOccurs="1" /> + <xs:element ref="match_list" maxOccurs="1" minOccurs="1" /> + + + </xs:sequence> + </xs:complexType> + + <xs:complexType name="identificationsType"> + <xs:annotation> + <xs:documentation> + list of identification elements + </xs:documentation> + </xs:annotation> + <xs:sequence> + <xs:element ref="identification" maxOccurs="unbounded" + minOccurs="0" /> + </xs:sequence> + </xs:complexType> + + <!-- <filter_params pep_evalue="0.05" prot_evalue="-3.0" pep_number="2" + filter_to_all="false" database_filter="contaminants_standarts.fasta" /> --> + <xs:complexType name="filter_paramsType"> + <xs:annotation> + <xs:documentation> + miscelaneous informations about this xtandem + pipeline run + </xs:documentation> + </xs:annotation> + <xs:attribute name="pep_evalue" type="xs:float"> + <xs:annotation> + <xs:documentation> + minimum peptide evalue + </xs:documentation> + </xs:annotation> + </xs:attribute> + <xs:attribute name="prot_evalue" type="xs:float"> + <xs:annotation> + <xs:documentation> + minimum protein evalue + </xs:documentation> + </xs:annotation> + </xs:attribute> + <xs:attribute name="pep_number" type="xs:int"> + <xs:annotation> + <xs:documentation> + minimum peptide number to validate a protein + </xs:documentation> + </xs:annotation> + </xs:attribute> + <xs:attribute name="filter_to_all" type="xs:boolean"> + </xs:attribute> + <xs:attribute name="database_filter" type="xs:string"> + </xs:attribute> + </xs:complexType> + + + <xs:simpleType name="Data_TypeType"> + <xs:annotation> + <xs:documentation> + the type of analyse used in XtandemPipeline + </xs:documentation> + </xs:annotation> + <xs:restriction base="xs:string"> + <xs:enumeration value="combi" /> + <xs:enumeration value="string" /> + <xs:enumeration value="date" /> + </xs:restriction> + </xs:simpleType> + + <!-- <information Data_Type="combi" match_number="5760" xtandem_pipeline_version="3.1.2"/> --> + <xs:complexType name="informationType"> + <xs:annotation> + <xs:documentation> + miscelaneous informations about this xtandem + pipeline run + </xs:documentation> + </xs:annotation> + <xs:attribute name="Data_Type" type="Data_TypeType" use="required"> + </xs:attribute> + <xs:attribute name="match_number" type="xs:int"> + <xs:annotation> + <xs:documentation> + number of match + </xs:documentation> + </xs:annotation> + </xs:attribute> + <xs:attribute name="xtandem_pipeline_version" type="xs:string"> + <xs:annotation> + <xs:documentation> + the xtandem pipeline version used to produce this + file + </xs:documentation> + </xs:annotation> + </xs:attribute> + </xs:complexType> + + + <xs:complexType name="xtandem_pipelineType"> + <xs:annotation> + <xs:documentation> + Root element of an XPIP file. + </xs:documentation> + </xs:annotation> + <xs:sequence> + <xs:element ref="information" maxOccurs="1" minOccurs="1" /> + <xs:element ref="filter_params" maxOccurs="1" minOccurs="1" /> + <xs:element ref="identifications" maxOccurs="1" minOccurs="1" /> + </xs:sequence> + <xs:attribute name="version" type="xs:string" use="required"> + <xs:annotation> + <xs:documentation> + Version of the current XPIP format. + </xs:documentation> + </xs:annotation> + </xs:attribute> + </xs:complexType> +</xs:schema> \ No newline at end of file diff --git a/xtandempipeline/doc/files/xpip/xpip_sample.xml b/xtandempipeline/doc/files/xpip/xpip_sample.xml new file mode 100644 index 000000000..cda3318a7 --- /dev/null +++ b/xtandempipeline/doc/files/xpip/xpip_sample.xml @@ -0,0 +1,62 @@ +<xtandem_pipeline xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:noNamespaceSchemaLocation="xpip.xsd" version="3.1.2"> + <information Data_Type="combi" match_number="5760" + xtandem_pipeline_version="3.1.2" /> + <filter_params pep_evalue="0.05" prot_evalue="-3.0" + pep_number="2" filter_to_all="false" database_filter="contaminants_standarts.fasta" /> + <identifications> + <identification> + <modifs_list_mass> + <modifs_mass modvalue="-18.0106" /> + <modifs_mass modvalue="-17.0265" /> + <modifs_mass modvalue="15.99" /> + <modifs_mass modvalue="42.0106" /> + <modifs_mass modvalue="57.04" /> + </modifs_list_mass> + <samples> + <sample value="2010_01_19_Pont_Lezica_Rafael_28_1_13_EENA1-13.xml" /> + <sample value="2009_10_19_Pont_Lezica_Rafael_20_1_45_EFM-9.xml" /> + </samples> + <match_list> + <match validate="false"> + <protein peptide_number="1972" evalue="-275.23846" + URL="contaminants_standarts.fasta" + description="conta|P04264|K2C1_HUMAN Keratin, type II cytoskeletal 1 (Cytokeratin 1) (K1) (CK 1) (67 kDa cytokeratin) (Hair alpha protein) - Homo sapiens (Human)."> + <protein_evalue evalue="-5.853872" + sample="20110323_Pontlezica_Raphael_1_B06_EFJ2-16.xml" /> + <protein_evalue evalue="-56.09546" + sample="2009_10_19_Pont_Lezica_Rafael_20_1_08_EFJ-8.xml" /> + <protein_evalue evalue="-29.321789" + sample="2010_01_19_Pont_Lezica_Rafael_28_1_54_EENB1-18.xml" /> + + + + + <sequence>SRQFSSRSGYRSGGGFSSGSAGIINYQRRTTSSSTRRSGGGGGRFSSCGGGGGSFGAGGGFGSRSLVNLGGSKSISISVARGGGRGSGFGGGYGGGGFGGGGFGGGGFGGGGIGGGGFGGFGSGGGGFGGGGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSREREQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEPYFESFINNLRRRVDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTNAENEFVTIKKDVDGAYMTKVDLQAKLDNLQQEIDFLTALYQAELSQMQTQISETNVILSMDNNRSLDLDSIIAEVKAQNEDIAQKSKAEAESLYQSKYEELQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISNLQQSISDAEQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEIATYRTLLEGEESRMSGECAPNVSVSVSTSHTTISGGGSRGGGGGGYGSGGSSYGSGGGSYGSGGGGGGGRGSYGSGGSSYGSGGGSYGSGGGGGGHGSYGSGSSSGGYRGGSGGGGGGSSGGRGSGGGSSGGSIGGRGSSSGGVKSSGGSSSVRFVSTTYSGVTR</sequence> + </protein> + <peptide_list> + <peptide sample="2009_10_19_Pont_Lezica_Rafael_20_1_01_EFJ-1.xml" + sample_file="/home/valot/analyse_en_cours/20110328_Douchet/Brachy_3/2009_10_19_Pont_Lezica_Rafael_20_1_01_EFJ-1.xml" + scan="602" scan_in_xtandem="602" RT="218" mhplus_obser="933.3101" + mhplus_theo="932.505" deltamass="0.805" sequence="SEIDNVKK" pre="QRLR" + post="QISN" start="409" stop="416" charge="2" evalue="0.0044" + hypercorr="39.3" validate="true"> + <modifs></modifs> + </peptide> + <peptide sample="2009_10_19_Pont_Lezica_Rafael_20_1_01_EFJ-1.xml" + sample_file="/home/valot/analyse_en_cours/20110328_Douchet/Brachy_3/2009_10_19_Pont_Lezica_Rafael_20_1_01_EFJ-1.xml" + scan="604" scan_in_xtandem="604" RT="219" mhplus_obser="1144.093" + mhplus_theo="1143.531" deltamass="0.563" sequence="KDVDGAYMTK" + pre="VTIK" post="VDLQ" start="288" stop="297" charge="2" evalue="5.0E-4" + hypercorr="44.6" validate="true"> + <modifs> + <modif aa="M" modvalue="15.99" posi="8" posi_in_prot="295" /> + </modifs> + </peptide> + + </peptide_list> + </match> + </match_list> + </identification> + </identifications> +</xtandem_pipeline> \ No newline at end of file -- GitLab