autouserguide
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autouserguide [2010/07/19 10:58] 132.168.73.9 |
autouserguide [2011/12/19 17:51] (current) 132.168.72.130 |
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| </parameters> | </parameters> | ||
| </delete.Proteins> | </delete.Proteins> | ||
| + | </code> | ||
| + | |||
| + | === Single match per query filter === | ||
| + | |||
| + | **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> | </code> | ||
| === Master protein filter === | === Master protein filter === | ||
| - | Nota : The "filter.master.rule.operation" parameter can be : | + | :!: 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 | ||
| Line 194: | Line 229: | ||
| </filter.Master> | </filter.Master> | ||
| </code> | </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.1279529920.txt.gz · Last modified: 2010/07/19 10:58 by 132.168.73.9
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