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autouserguide [2009/12/07 14:34] 132.168.73.9 |
autouserguide [2011/12/19 17:51] (current) 132.168.72.130 |
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| /script:"[Path\To\IRMaScripts]\script_TEST_DB.xml" | /script:"[Path\To\IRMaScripts]\script_TEST_DB.xml" | ||
| - | * [Path\To\IRMaVBScripts] : to be replaced by the absolute path to directory where VBScript are stored. | + | * [Path\To\IRMaVBScripts] : to be replaced by the absolute path to directory where VBScript are stored. It is RECOMMENDED to create a directory for each version of IRMa in order to be sure to use appropriated scripts. |
| * [Path\To\IRMaScripts] : to be replaced by the absolute path to directory where IRMa instruction scripts are stored. | * [Path\To\IRMaScripts] : to be replaced by the absolute path to directory where IRMa instruction scripts are stored. | ||
| * <cachedpeaklist> and <resultfilename> are automatically replaced by, respectively, the full path to generated MGF (if a Data Import Filter has been specified in task) and the Mascot Result file. | * <cachedpeaklist> and <resultfilename> are automatically replaced by, respectively, the full path to generated MGF (if a Data Import Filter has been specified in task) and the Mascot Result file. | ||
| + | ==== Scripts ==== | ||
| + | Scripts are written in XML format. XML format That is, very simply, a set of blocs (nested or successive) with a opening and closing tag... | ||
| - | ==== Scripts ==== | + | <code> |
| + | <script> // Opening tag for script bloc | ||
| + | ... // bloc content | ||
| + | </script> // closing tag for script bloc | ||
| + | </code> | ||
| + | Every script should be described in a script bloc, as shown above. A script is a set of actions corresponding to IRMa operation to be executed. The execution order of these operations will be identical to the action description order in the script file. | ||
| + | === Mascot result parse === | ||
| + | |||
| + | This opération is only possible on Mascot identification and not on previously saved IRMa project (.irma). This action correspond to the execution of Mascot parse in IRMa using same parameters as those entered in Report Settings/Parser Properties dialog | ||
| + | |||
| + | //Parse// bloc is defined as follow : ''parse'' tag, followed by a ''parameters'' tag which contains all parameters to be used. Each parameter is described in a ''parameter'' tag and a name and value should be specified. | ||
| + | |||
| + | __Parse bloc example:__ | ||
| <code xml> | <code xml> | ||
| - | <filter.Master> | + | <parse> |
| <parameters> | <parameters> | ||
| - | <parameter name="filter.master.rule.map"> | + | <parameter name="is.hit.count.auto"> |
| - | <value class="map"> | + | <value class="boolean">true</value> |
| - | <entry> | + | |
| - | <string>R1</string> | + | |
| - | <cea.irma.model.validation.MasterProteinFilterRule> | + | |
| - | <properties> | + | |
| - | <entry> | + | |
| - | <string>filter.master.rule.operation</string> | + | |
| - | <parameter name="filter.master.rule.operation"> | + | |
| - | <value class="cea.irma.model.validation.MasterProteinFilterRule$RuleOperation">CONTAINS_RULE</value> | + | |
| - | </parameter> | + | |
| - | </entry> | + | |
| - | <entry> | + | |
| - | <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> | + | |
| - | <entry> | + | |
| - | <string>filter.master.rule.name</string> | + | |
| - | <parameter name="filter.master.rule.name"> | + | |
| - | <value class="string">R1</value> | + | |
| - | </parameter> | + | |
| - | </entry> | + | |
| - | </properties> | + | |
| - | </cea.irma.model.validation.MasterProteinFilterRule> | + | |
| - | </entry> | + | |
| - | </value> | + | |
| </parameter> | </parameter> | ||
| - | <parameter name="filter.master.rules.composition"> | + | <parameter name="protein.cutoff"> |
| - | <value class="string">R1</value> | + | <value class="double">0.05</value> |
| + | </parameter> | ||
| + | <parameter name="ions.score.cutoff"> | ||
| + | <value class="int">0</value> | ||
| + | </parameter> | ||
| + | <parameter name="subset.threshold"> | ||
| + | <value class="double">0.5</value> | ||
| + | </parameter> | ||
| + | <parameter name="read.sequence"> | ||
| + | <value class="string">masters</value> | ||
| </parameter> | </parameter> | ||
| </parameters> | </parameters> | ||
| + | </parse> | ||
| + | </code> | ||
| + | |||
| + | __Available parameters:__ | ||
| + | * name: ''is.hit.count.auto''; allowed values ''false'' or ''true'' ; Specify how to obtain the hits list, with an absolute number of hit (false) or specifying a p value (true) | ||
| + | * name: ''protein.cutoff''; double value; Specify the p value to use to obtain the hits list. parameter used if ''is.hit.count.auto'' = true | ||
| + | * name: ''hit.count''; integer value; Specify the number of hit to get. parameter used if ''is.hit.count.auto'' = false | ||
| + | * name: ''ions.score.cutoff''; integer value; Specify the peptide score threshold - only peptides with a higher score will be considered- | ||
| + | * name: ''subset.threshold''; integer value ; Specify the threshold to used in order to import subset proteins. to import a subset protein the following rule should be verified : Subset_Prot_score >= Master_Prot_score * (1-subset.threshold) | ||
| + | * name: ''read.sequence''; allowed values: ''never'', ''masters'' ou ''always''; Specify the rule to use to read protein sequence (get sequence only if present in identification result file, get sequence from mascot server for master proteins if necessary, get sequence from mascot server for all proteins) | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | === Peptide specific and score filter === | ||
| + | |||
| + | <code xml> | ||
| + | <delete.Proteins> | ||
| + | <parameters> | ||
| + | <parameter name="is.freeze.fp.analysis"> | ||
| + | <value class="boolean">true</value> | ||
| + | </parameter> | ||
| + | <parameter name="peptides.count"> | ||
| + | <value class="int">1</value> | ||
| + | </parameter> | ||
| + | <parameter name="peptides.score"> | ||
| + | <value class="int">20</value> | ||
| + | </parameter> | ||
| + | <parameter name="peptides.unicity"> | ||
| + | <value class="boolean">true</value> | ||
| + | </parameter> | ||
| + | </parameters> | ||
| + | </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> | ||
| + | |||
| + | === 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 | ||
| + | * NOT_CONTAINS_RULE | ||
| + | * BEGINS_WITH_RULE | ||
| + | * ENDS_WITH_RULE | ||
| + | |||
| + | __Simple Rule 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> | ||
| + | </rules.list> | ||
| + | <rules.composition value="R1"/> | ||
| </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.1260192897.txt.gz · Last modified: 2009/12/07 14:34 by 132.168.73.9
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