xiFDR/nbactions-csv commandline.xml at master · lutzfischer/xiFDR · GitHub

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<?xml version="1.0" encoding="UTF-8"?>
<actions>
        <action>
            <actionName>run</actionName>
            <packagings>
                <packaging>jar</packaging>
            </packagings>
            <goals>
                <goal>process-classes</goal>
                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
            </goals>
            <properties>
                <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
                <exec.executable>java</exec.executable>
                <exec.workingdir></exec.workingdir>
                <exec.appArgs>--dbids=14107 --filter="(scoreP1Coverage &gt;= 4 AND (pepSeq2 is null OR  scoreP2Coverage &gt;= 4 )) AND (deltaScore &gt;= Score/2.5) AND (pepSeq2 is not null) AND (mgxrank &lt;= 3)" --psmfdr=100 --pepfdr=100 --proteinfdr=100 --linkfdr=100 --ppifdr=100 --csvOutDir=/data/rappstore/new_storage/fschimweg/xiSearch/myco-dss --csvBaseName=14107 --connection=jdbc:postgresql://xidb.bioanalytik.tu-berlin.de:5432/xi3 --user=bio_user --password=bio1sTheUs3r</exec.appArgs>
                <exec.vmArgs>-Dfile.encoding=UTF-8 --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED -Xmx4G</exec.vmArgs>
                <exec.mainClass>org.rappsilber.fdr.DBinFDR</exec.mainClass>
            </properties>
        </action>
        <action>
            <actionName>debug</actionName>
            <packagings>
                <packaging>jar</packaging>
            </packagings>
            <goals>
                <goal>process-classes</goal>
                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
            </goals>
            <properties>
                <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
                <exec.executable>java</exec.executable>
                <jpda.listen>true</jpda.listen>
                <exec.workingdir></exec.workingdir>
                <exec.appArgs>--dbids=14107 --filter="(scoreP1Coverage &gt;= 4 AND (pepSeq2 is null OR  scoreP2Coverage &gt;= 4 )) AND (deltaScore &gt;= Score/2.5) AND (pepSeq2 is not null) AND (mgxrank &lt;= 3)" --psmfdr=100 --pepfdr=100 --proteinfdr=100 --linkfdr=100 --ppifdr=100 --csvOutDir=/data/rappstore/new_storage/fschimweg/xiSearch/myco-dss --csvBaseName=14107 --connection=jdbc:postgresql://xidb.bioanalytik.tu-berlin.de:5432/xi3 --user=bio_user --password=bio1sTheUs3r</exec.appArgs>
                <exec.vmArgs>-Dfile.encoding=UTF-8 --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED -Xmx4G -agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
                <exec.mainClass>org.rappsilber.fdr.DBinFDR</exec.mainClass>
            </properties>
        </action>
        <action>
            <actionName>profile</actionName>
            <packagings>
                <packaging>jar</packaging>
            </packagings>
            <goals>
                <goal>process-classes</goal>
                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
            </goals>
            <properties>
                <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
                <exec.executable>java</exec.executable>
                <exec.workingdir></exec.workingdir>
                <exec.appArgs>--dbids=14107 --filter="(scoreP1Coverage &gt;= 4 AND (pepSeq2 is null OR  scoreP2Coverage &gt;= 4 )) AND (deltaScore &gt;= Score/2.5) AND (pepSeq2 is not null) AND (mgxrank &lt;= 3)" --psmfdr=100 --pepfdr=100 --proteinfdr=100 --linkfdr=100 --ppifdr=100 --csvOutDir=/data/rappstore/new_storage/fschimweg/xiSearch/myco-dss --csvBaseName=14107 --connection=jdbc:postgresql://xidb.bioanalytik.tu-berlin.de:5432/xi3 --user=bio_user --password=bio1sTheUs3r</exec.appArgs>
                <exec.vmArgs>-Dfile.encoding=UTF-8 --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED -Xmx4G</exec.vmArgs>
                <exec.mainClass>org.rappsilber.fdr.DBinFDR</exec.mainClass>
            </properties>
        </action>
    </actions>