autouserguide
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autouserguide [2010/03/01 07:25] 132.168.73.247 |
autouserguide [2011/12/19 17:51] (current) 132.168.72.130 |
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| __Parse bloc example:__ | __Parse bloc example:__ | ||
| - | <code> | + | <code xml> |
| <parse> | <parse> | ||
| <parameters> | <parameters> | ||
| Line 118: | Line 118: | ||
| </code> | </code> | ||
| - | === Peptide specific and score filter === | + | === Single match per query filter === |
| - | Nota : The "filter.master.rule.operation" parameter can be : | + | |
| + | **Nota** : no parameter to set. | ||
| + | |||
| + | <code xml> | ||
| + | <filter.PSM> | ||
| + | <parameter name="filter.class.name"> | ||
| + | <value class="string">cea.irma.model.validation.SingleMatchPerQueryFilter</value> | ||
| + | </parameter> | ||
| + | </filter.PSM> | ||
| + | </code> | ||
| + | |||
| + | === FPR seeker filter === | ||
| + | |||
| + | * FPR = False Positive Rate | ||
| + | * SaR = Score and Rank | ||
| + | * DM = Delta Mass | ||
| + | See inside xml below to find comments: | ||
| + | <code xml> | ||
| + | <filter.FPR.Seeker> | ||
| + | <parameters> | ||
| + | <parameter name="seek.fpr.with.score.and.rank.filter"> | ||
| + | <value class="boolean">true</value> <!-- true : the SaR filter will be used. Set to false if you juste want DM to be used. If both are set to false, the default one (SaR) will be used--> | ||
| + | </parameter> | ||
| + | <parameter name="seek.fpr.with.delta.mass.filter"> | ||
| + | <value class="boolean">true</value> <!-- true : the DM filter will be used. Set to false if you juste want SaR to be used. If both are set to false, the default one (SaR) will be used--> | ||
| + | </parameter> | ||
| + | <parameter name="sought.fpr.in.percentage"> | ||
| + | <value class="double">1.0</value> | ||
| + | </parameter> | ||
| + | </parameters> | ||
| + | </filter.FPR.Seeker> | ||
| + | </code> | ||
| + | |||
| + | === Master protein filter === | ||
| + | :!: If the master protein change is leading to an ambiguous peptide suppression (because the new master protein don't have match with it), the script will suppress it. It's a different behaviour than manual master protein changing in IRMa application, where a dialog ask the user to decide what to do.\\ | ||
| + | :!: The "filter.master.rule.operation" parameter can be : | ||
| * CONTAINS_RULE | * CONTAINS_RULE | ||
| * NOT_CONTAINS_RULE | * NOT_CONTAINS_RULE | ||
| * BEGINS_WITH_RULE | * BEGINS_WITH_RULE | ||
| * ENDS_WITH_RULE | * ENDS_WITH_RULE | ||
| + | |||
| + | __Simple Rule example:__ | ||
| <code xml> | <code xml> | ||
| <filter.Master> | <filter.Master> | ||
| - | <parameters> | + | <rules.list> |
| - | <parameter name="filter.master.rule.map"> <!-- FIRST Parameter : A collection of rule --> | + | <rule name="R1"> |
| - | <value class="map"> | + | <parameter name="filter.master.rule.operation"> |
| - | <entry> | + | <value class="rule.operation">ENDS_WITH_RULE</value> |
| - | <string>R1</string> | + | </parameter> |
| - | <cea.irma.model.validation.MasterProteinFilterRule> | + | <parameter name="filter.master.applies.to.description"> |
| - | <properties> | + | <value class="boolean">false</value> |
| - | <entry> | + | </parameter> |
| - | <string>filter.master.rule.name</string> | + | <parameter name="filter.master.applies.to.accession"> |
| - | <parameter name="filter.master.rule.name"> | + | <value class="boolean">true</value> |
| - | <value class="string">R1</value> | + | </parameter> |
| - | </parameter> | + | <parameter name="filter.master.searched.string"> |
| - | </entry> | + | <value class="string">_HUMAN</value> |
| - | <entry> | + | </parameter> |
| - | <string>filter.master.rule.operation</string> | + | <parameter name="filter.master.rule.name"> |
| - | <parameter name="filter.master.rule.operation"> | + | <value class="string">R1</value> |
| - | <value class="cea.irma.model.validation.MasterProteinFilterRule$RuleOperation">CONTAINS_RULE</value> | + | </parameter> |
| - | </parameter> | + | </rule> |
| - | </entry> | + | </rules.list> |
| - | <entry> | + | <rules.composition value="R1"/> |
| - | <string>filter.master.applies.accession</string> | + | |
| - | <parameter name="filter.master.applies.accession"> | + | |
| - | <value class="boolean">true</value> | + | |
| - | </parameter> | + | |
| - | </entry> | + | |
| - | <entry> | + | |
| - | <string>filter.master.applies.description</string> | + | |
| - | <parameter name="filter.master.applies.description"> | + | |
| - | <value class="boolean">false</value> | + | |
| - | </parameter> | + | |
| - | </entry> | + | |
| - | <entry> | + | |
| - | <string>filter.master.searched.string</string> | + | |
| - | <parameter name="filter.master.searched.string"> | + | |
| - | <value class="string">_HUMAN</value> | + | |
| - | </parameter> | + | |
| - | </entry> | + | |
| - | </properties> | + | |
| - | </cea.irma.model.validation.MasterProteinFilterRule> | + | |
| - | </entry> | + | |
| - | </value> | + | |
| - | </parameter> <!-- END of FIRST Parameter --> | + | |
| - | <parameter name="filter.master.rules.composition"> <!-- SECOND Parameter : The composition of rules previously set --> | + | |
| - | <value class="string">R1</value> | + | |
| - | </parameter> | + | |
| - | </parameters> <!-- END of SECOND Parameter --> | + | |
| </filter.Master> | </filter.Master> | ||
| </code> | </code> | ||
| + | __Dual rules example:__ | ||
| + | |||
| + | <code xml> | ||
| + | <filter.Master> | ||
| + | <rules.list> | ||
| + | <rule name="R1"> | ||
| + | <parameter name="filter.master.rule.operation"> | ||
| + | <value class="rule.operation">ENDS_WITH_RULE</value> | ||
| + | </parameter> | ||
| + | <parameter name="filter.master.applies.to.description"> | ||
| + | <value class="boolean">false</value> | ||
| + | </parameter> | ||
| + | <parameter name="filter.master.applies.to.accession"> | ||
| + | <value class="boolean">true</value> | ||
| + | </parameter> | ||
| + | <parameter name="filter.master.searched.string"> | ||
| + | <value class="string">_HUMAN</value> | ||
| + | </parameter> | ||
| + | <parameter name="filter.master.rule.name"> | ||
| + | <value class="string">R1</value> | ||
| + | </parameter> | ||
| + | </rule> | ||
| + | <rule name="R2"> | ||
| + | <parameter name="filter.master.rule.operation"> | ||
| + | <value class="rule.operation">NOT_CONTAINS_RULE</value> | ||
| + | </parameter> | ||
| + | <parameter name="filter.master.applies.to.description"> | ||
| + | <value class="boolean">true</value> | ||
| + | </parameter> | ||
| + | <parameter name="filter.master.applies.to.accession"> | ||
| + | <value class="boolean">false</value> | ||
| + | </parameter> | ||
| + | <parameter name="filter.master.searched.string"> | ||
| + | <value class="string">tr</value> | ||
| + | </parameter> | ||
| + | <parameter name="filter.master.rule.name"> | ||
| + | <value class="string">R2</value> | ||
| + | </parameter> | ||
| + | </rule> | ||
| + | </rules.list> | ||
| + | <rules.composition value="R1 and R2"/> | ||
| + | </filter.Master> | ||
| + | </code> | ||
| + | |||
| + | |||
| + | === MGF Export === | ||
| + | * Parameters | ||
| + | * Result MGF destination directory | ||
| + | * The other parameters (what data will be export) are taken from java_option, so this data must be set in IRMa application (Tools => Preferences => Queries export) before using the script | ||
| + | * The result MGF file will be named as the "sourcefile" information contains in the identification. If this "sourcefile" has been a MGF file no name transformation is done, if not the extension will be change to ".mgf" | ||
| + | * No possibility, as in IRMa application to choose a corresponding mgf to generate a new one. This script is based only on information contained in the identification | ||
| + | |||
| + | <code xml><export.MGF baseFilePath="Path/to/export/directory" /></code> | ||
| + | |||
| + | === Database Export === | ||
| + | * Parameters | ||
| + | * for "export.DB", the parameter **"version"** is optional. Its value can be "D" or "E" (default) depending of the version of MSIdb you want to export to. If no parameter is given or if its value is different from the two accepted the default one will be chosen. | ||
| + | <code xml> | ||
| + | <export.DB dbVersion="E"> | ||
| + | <config> | ||
| + | <parameters> | ||
| + | <parameter name="db.export.user"> | ||
| + | <value class="string">username</value> | ||
| + | </parameter> | ||
| + | <parameter name="db.export.pswd"> | ||
| + | <value class="string">passwd</value> | ||
| + | </parameter> | ||
| + | <parameter name="db.export.driver"> | ||
| + | <value class="string">org.postgresql.Driver</value> | ||
| + | </parameter> | ||
| + | <parameter name="db.export.dbname"> | ||
| + | <value class="string">MSIdb_Name</value> | ||
| + | </parameter> | ||
| + | <parameter name="db.export.url"> | ||
| + | <value class="string">jdbc:postgresql://DB_Server_Address:DB_Server_Port/MSIdb_Name</value> | ||
| + | </parameter> | ||
| + | <parameter name="db.export.unassigned.peptides"> | ||
| + | <value class="boolean">false</value> | ||
| + | </parameter> | ||
| + | <parameter name="db.export.unassigned.queries"> | ||
| + | <value class="boolean">false</value> | ||
| + | </parameter> | ||
| + | </parameters> | ||
| + | </config> | ||
| + | </export.DB> | ||
| + | </code> | ||
autouserguide.1267424742.txt.gz · Last modified: 2010/03/01 07:25 by 132.168.73.247
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