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Commit 8d8a4fe3 authored by langella's avatar langella
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new xml schema for XPIP 

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@189 b8ef2a07-7df7-436f-90b9-41648038564b
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xtandempipeline/doc/files/xpip/xpip.xsd 0 → 100644
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<?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
xtandempipeline/doc/files/xpip/xpip_sample.xml 0 → 100644
+ 62
− 0
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<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
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