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4.7.7a peptide parameters #97

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4.7.7a peptide parameters #97

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ce56080
initial commit of the peptide parameters metanode
Heriette Mar 6, 2024
e982cb1
Peptide parameters 2.0.0 - added metanode description
Heriette Mar 7, 2024
a6609f4
Peptide parameters 2.1.0 - fixed checking validity of peptide sequence
Heriette May 16, 2024
ab3a8de
Peptide parameters 2.2.0 - added extra output containing unprocessed …
Heriette May 17, 2024
d29dfec
Peptide parameters 2.3.0 - fixed error with column selection
Heriette Jun 11, 2024
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4 changes: 4 additions & 0 deletions Metanodes templates/__Other__/Peptide parameters/.savedWithData
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Do not delete this file!
This file serves to indicate that the workflow was written as part of the usual save routine (not exported).

Workflow was last saved by user knimeuser on Tue Jun 11 15:46:05 CEST 2024
219 changes: 219 additions & 0 deletions Metanodes templates/__Other__/Peptide parameters/Column Filter (#1701)/settings.xml
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63 changes: 63 additions & 0 deletions Metanodes templates/__Other__/Peptide parameters/Column Rename _Regex_ (#1705)/settings.xml
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<?xml version="1.0" encoding="UTF-8"?>
<config xmlns="http://www.knime.org/2008/09/XMLConfig" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.knime.org/2008/09/XMLConfig http://www.knime.org/XMLConfig_2008_09.xsd" key="settings.xml">
<entry key="node_file" type="xstring" value="settings.xml"/>
<config key="flow_stack"/>
<config key="internal_node_subsettings">
<entry key="memory_policy" type="xstring" value="CacheSmallInMemory"/>
</config>
<config key="model">
<entry key="searchString" type="xstring" value="(.+)"/>
<entry key="replaceString" type="xstring" value=""/>
<entry key="isCaseInsensitive" type="xboolean" value="false"/>
<entry key="isLiteral" type="xboolean" value="false"/>
</config>
<config key="variables">
<entry key="version" type="xstring" value="V_2019_09_13"/>
<config key="tree">
<config key="replaceString">
<entry key="used_variable" type="xstring" value="prefix_regex"/>
<entry key="exposed_variable" type="xstring" isnull="true" value=""/>
</config>
</config>
</config>
<config key="nodeAnnotation">
<entry key="text" type="xstring" value="add prefix"/>
<entry key="bgcolor" type="xint" value="16777215"/>
<entry key="x-coordinate" type="xint" value="449"/>
<entry key="y-coordinate" type="xint" value="259"/>
<entry key="width" type="xint" value="142"/>
<entry key="height" type="xint" value="17"/>
<entry key="alignment" type="xstring" value="CENTER"/>
<entry key="borderSize" type="xint" value="0"/>
<entry key="borderColor" type="xint" value="16777215"/>
<entry key="defFontSize" type="xint" value="10"/>
<entry key="annotation-version" type="xint" value="20151123"/>
<config key="styles"/>
</config>
<entry key="customDescription" type="xstring" isnull="true" value=""/>
<entry key="state" type="xstring" value="IDLE"/>
<entry key="factory" type="xstring" value="org.knime.base.node.preproc.columnrenameregex.ColumnRenameRegexNodeFactory"/>
<entry key="node-name" type="xstring" value="Column Rename (Regex)"/>
<entry key="node-bundle-name" type="xstring" value="KNIME Base Nodes"/>
<entry key="node-bundle-symbolic-name" type="xstring" value="org.knime.base"/>
<entry key="node-bundle-vendor" type="xstring" value="KNIME AG, Zurich, Switzerland"/>
<entry key="node-bundle-version" type="xstring" value="4.7.7.v202308021457"/>
<entry key="node-feature-name" type="xstring" value="KNIME Base nodes"/>
<entry key="node-feature-symbolic-name" type="xstring" value="org.knime.features.base.feature.group"/>
<entry key="node-feature-vendor" type="xstring" value="KNIME AG, Zurich, Switzerland"/>
<entry key="node-feature-version" type="xstring" value="4.7.7.v202308161346"/>
<config key="factory_settings"/>
<entry key="name" type="xstring" value="Column Rename (Regex)"/>
<entry key="hasContent" type="xboolean" value="false"/>
<entry key="isInactive" type="xboolean" value="false"/>
<config key="ports">
<config key="port_1">
<entry key="index" type="xint" value="1"/>
<entry key="port_dir_location" type="xstring" isnull="true" value=""/>
</config>
</config>
<config key="filestores">
<entry key="file_store_location" type="xstring" isnull="true" value=""/>
<entry key="file_store_id" type="xstring" isnull="true" value=""/>
</config>
</config>
142 changes: 142 additions & 0 deletions ...emplates/__Other__/Peptide parameters/Column Selection Configuration (#1627)/settings.xml
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<?xml version="1.0" encoding="UTF-8"?>
<config xmlns="http://www.knime.org/2008/09/XMLConfig" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.knime.org/2008/09/XMLConfig http://www.knime.org/XMLConfig_2008_09.xsd" key="settings.xml">
<entry key="node_file" type="xstring" value="settings.xml"/>
<config key="flow_stack"/>
<config key="internal_node_subsettings">
<entry key="memory_policy" type="xstring" value="CacheSmallInMemory"/>
</config>
<config key="model">
<config key="defaultValue">
<entry key="column" type="xstring" value="Stripped.Sequence"/>
</config>
<entry key="hideInDialog" type="xboolean" value="false"/>
<entry key="parameterName" type="xstring" value="aa_column"/>
<entry key="label" type="xstring" value="Select column containing AA sequences"/>
<entry key="description" type="xstring" value="Enter Description"/>
<entry key="required" type="xboolean" value="true"/>
<entry key="flowVariableName" type="xstring" value="aa_column"/>
<config key="possibleColumns">
<entry key="array-size" type="xint" value="56"/>
<entry key="0" type="xstring" value="File.Name"/>
<entry key="1" type="xstring" value="Run"/>
<entry key="2" type="xstring" value="Protein.Group"/>
<entry key="3" type="xstring" value="Protein.Ids"/>
<entry key="4" type="xstring" value="Protein.Names"/>
<entry key="5" type="xstring" value="Genes"/>
<entry key="6" type="xstring" value="PG.Quantity"/>
<entry key="7" type="xstring" value="PG.Normalised"/>
<entry key="8" type="xstring" value="PG.MaxLFQ"/>
<entry key="9" type="xstring" value="Genes.Quantity"/>
<entry key="10" type="xstring" value="Genes.Normalised"/>
<entry key="11" type="xstring" value="Genes.MaxLFQ"/>
<entry key="12" type="xstring" value="Genes.MaxLFQ.Unique"/>
<entry key="13" type="xstring" value="Modified.Sequence"/>
<entry key="14" type="xstring" value="Stripped.Sequence"/>
<entry key="15" type="xstring" value="Precursor.Id"/>
<entry key="16" type="xstring" value="Precursor.Charge"/>
<entry key="17" type="xstring" value="Q.Value"/>
<entry key="18" type="xstring" value="PEP"/>
<entry key="19" type="xstring" value="Global.Q.Value"/>
<entry key="20" type="xstring" value="Protein.Q.Value"/>
<entry key="21" type="xstring" value="PG.Q.Value"/>
<entry key="22" type="xstring" value="Global.PG.Q.Value"/>
<entry key="23" type="xstring" value="GG.Q.Value"/>
<entry key="24" type="xstring" value="Translated.Q.Value"/>
<entry key="25" type="xstring" value="Proteotypic"/>
<entry key="26" type="xstring" value="Precursor.Quantity"/>
<entry key="27" type="xstring" value="Precursor.Normalised"/>
<entry key="28" type="xstring" value="Precursor.Translated"/>
<entry key="29" type="xstring" value="Ms1.Translated"/>
<entry key="30" type="xstring" value="Quantity.Quality"/>
<entry key="31" type="xstring" value="RT"/>
<entry key="32" type="xstring" value="RT.Start"/>
<entry key="33" type="xstring" value="RT.Stop"/>
<entry key="34" type="xstring" value="iRT"/>
<entry key="35" type="xstring" value="Predicted.RT"/>
<entry key="36" type="xstring" value="Predicted.iRT"/>
<entry key="37" type="xstring" value="Lib.Q.Value"/>
<entry key="38" type="xstring" value="Lib.PG.Q.Value"/>
<entry key="39" type="xstring" value="Ms1.Profile.Corr"/>
<entry key="40" type="xstring" value="Ms1.Area"/>
<entry key="41" type="xstring" value="Evidence"/>
<entry key="42" type="xstring" value="Spectrum.Similarity"/>
<entry key="43" type="xstring" value="Mass.Evidence"/>
<entry key="44" type="xstring" value="CScore"/>
<entry key="45" type="xstring" value="Decoy.Evidence"/>
<entry key="46" type="xstring" value="Decoy.CScore"/>
<entry key="47" type="xstring" value="Fragment.Quant.Raw"/>
<entry key="48" type="xstring" value="Fragment.Quant.Corrected"/>
<entry key="49" type="xstring" value="Fragment.Correlations"/>
<entry key="50" type="xstring" value="MS2.Scan"/>
<entry key="51" type="xstring" value="IM"/>
<entry key="52" type="xstring" value="iIM"/>
<entry key="53" type="xstring" value="Predicted.IM"/>
<entry key="54" type="xstring" value="Predicted.iIM"/>
<entry key="55" type="xstring" value="deltaRT"/>
</config>
<entry key="type" type="xstring" value="Dropdown"/>
<entry key="limit_number_visible_options" type="xboolean" value="false"/>
<entry key="number_visible_options" type="xint" value="10"/>
<config key="input_filter">
<config key="type_filter">
<entry key="org.knime.core.data.StringValue" type="xboolean" value="true"/>
<entry key="org.knime.core.data.DoubleValue" type="xboolean" value="false"/>
<entry key="org.knime.core.data.IntValue" type="xboolean" value="false"/>
<entry key="org.knime.core.data.BooleanValue" type="xboolean" value="false"/>
<entry key="org.knime.core.data.LongValue" type="xboolean" value="false"/>
<entry key="org.knime.core.data.time.localdatetime.LocalDateTimeValue" type="xboolean" value="false"/>
</config>
<entry key="allow_all_types" type="xboolean" value="true"/>
<entry key="filter_columns_without_domain" type="xboolean" value="false"/>
</config>
</config>
<config key="nodeAnnotation">
<entry key="text" type="xstring" value="select%%00010sequence column"/>
<entry key="bgcolor" type="xint" value="16777215"/>
<entry key="x-coordinate" type="xint" value="-191"/>
<entry key="y-coordinate" type="xint" value="118"/>
<entry key="width" type="xint" value="142"/>
<entry key="height" type="xint" value="32"/>
<entry key="alignment" type="xstring" value="CENTER"/>
<entry key="borderSize" type="xint" value="0"/>
<entry key="borderColor" type="xint" value="16777215"/>
<entry key="defFontSize" type="xint" value="10"/>
<entry key="annotation-version" type="xint" value="20151123"/>
<config key="styles">
<config key="style_0">
<entry key="start" type="xint" value="0"/>
<entry key="length" type="xint" value="22"/>
<entry key="fontname" type="xstring" value="Sans"/>
<entry key="fontstyle" type="xint" value="0"/>
<entry key="fontsize" type="xint" value="10"/>
<entry key="fgcolor" type="xint" value="0"/>
</config>
</config>
</config>
<entry key="customDescription" type="xstring" isnull="true" value=""/>
<entry key="state" type="xstring" value="IDLE"/>
<entry key="factory" type="xstring" value="org.knime.js.base.node.configuration.selection.column.ColumnSelectionDialogNodeFactory2"/>
<entry key="node-name" type="xstring" value="Column Selection Configuration"/>
<entry key="node-bundle-name" type="xstring" value="KNIME Quick Form Nodes"/>
<entry key="node-bundle-symbolic-name" type="xstring" value="org.knime.js.quickforms"/>
<entry key="node-bundle-vendor" type="xstring" value="KNIME AG, Zurich, Switzerland"/>
<entry key="node-bundle-version" type="xstring" value="4.7.0.v202302071224"/>
<entry key="node-feature-name" type="xstring" value="KNIME Quick Forms"/>
<entry key="node-feature-symbolic-name" type="xstring" value="org.knime.features.js.quickforms.feature.group"/>
<entry key="node-feature-vendor" type="xstring" value="KNIME AG, Zurich, Switzerland"/>
<entry key="node-feature-version" type="xstring" value="4.7.4.v202306091222"/>
<config key="factory_settings"/>
<entry key="name" type="xstring" value="Column Selection Configuration"/>
<entry key="hasContent" type="xboolean" value="false"/>
<entry key="isInactive" type="xboolean" value="false"/>
<config key="ports">
<config key="port_1">
<entry key="index" type="xint" value="1"/>
<entry key="port_dir_location" type="xstring" isnull="true" value=""/>
</config>
</config>
<config key="filestores">
<entry key="file_store_location" type="xstring" isnull="true" value=""/>
<entry key="file_store_id" type="xstring" isnull="true" value=""/>
</config>
</config>
74 changes: 74 additions & 0 deletions Metanodes templates/__Other__/Peptide parameters/Component Input (#1618)/settings.xml
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<?xml version="1.0" encoding="UTF-8"?>
<config xmlns="http://www.knime.org/2008/09/XMLConfig" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.knime.org/2008/09/XMLConfig http://www.knime.org/XMLConfig_2008_09.xsd" key="settings.xml">
<entry key="node_file" type="xstring" value="settings.xml"/>
<config key="flow_stack"/>
<config key="internal_node_subsettings">
<entry key="memory_policy" type="xstring" value="CacheSmallInMemory"/>
</config>
<config key="model">
<config key="variable-filter">
<entry key="filter-type" type="xstring" value="STANDARD"/>
<config key="included_names">
<entry key="array-size" type="xint" value="0"/>
</config>
<config key="excluded_names">
<entry key="array-size" type="xint" value="0"/>
</config>
<entry key="enforce_option" type="xstring" value="EnforceInclusion"/>
<config key="name_pattern">
<entry key="pattern" type="xstring" value=""/>
<entry key="type" type="xstring" value="Wildcard"/>
<entry key="caseSensitive" type="xboolean" value="true"/>
<entry key="excludeMatching" type="xboolean" value="false"/>
</config>
</config>
<entry key="variable-prefix" type="xstring" isnull="true" value=""/>
<config key="port-names">
<entry key="array-size" type="xint" value="1"/>
<entry key="0" type="xstring" value="Input table"/>
</config>
<config key="port-descriptions">
<entry key="array-size" type="xint" value="1"/>
<entry key="0" type="xstring" value="Input table containing a sequence column for the calculation of selected peptide parameters"/>
</config>
<entry key="sub-node-description" type="xstring" value="Metanode for the calculation of theoretical peptide parameters based on their amino acid sequence as implemented in the Peptides R package (Osorio et al., 2015). Note that it is only possible to use an amino acid sequence without post-translational modifications information.%%00010%%00010=================%%00010%%00010Used programs and tools and their respective licenses at the time of the metanode creation. Version numbers and the licenses might differ based on your local installation. Please inspect your local installation and contact us if you can not locate your local version and or license terms.%%00010%%00010KNIME nodes (The KNIME nodes consist of the following GNU GPL 3.0 License. Licence terms are available here: https://www.gnu.org/licenses/gpl.html)%%00010R 4.2.0 (The R consists of the following GPL-3 License. License terms are available here: https://www.r-project.org/Licenses/GPL-3)%%00010Peptides (R package) (This package uses the GPL-2 License. License terms are available here: https://cran.r-project.org/web/licenses/GPL-2)%%00010Python 3 (The Python consists of the following Python 3.6 License. Licence terms are available here: https://docs.python.org/3.6/license.html) %%00010%%00010The metanode was created in KNIME 4.7.7 running inside the docker image (https://hub.docker.com/r/cfprot/knime/), tag 4.7.7a.%%00010%%00010=================%%00010%%00010This version of metanode is available under the GNU GPL 3.0 License, unless stated otherwise. The full version of the license terms is available at https://www.gnu.org/licenses/gpl.html.%%00010Version: 2.3.0 from 2024-06-11%%00010Contact person: Karolina Krystofova (karolina.krystofova@ceitec.muni.cz)%%00010More information can be found at https://github.com/OmicsWorkflows/KNIME_metanodes."/>
</config>
<entry key="customDescription" type="xstring" isnull="true" value=""/>
<entry key="state" type="xstring" value="IDLE"/>
<config key="nodecontainer_message">
<entry key="type" type="xstring" value="WARNING"/>
<entry key="message" type="xstring" value="Component does not have input data, execute upstream nodes first"/>
</config>
<entry key="isDeletable" type="xboolean" value="false"/>
<entry key="factory" type="xstring" value="org.knime.core.node.workflow.virtual.subnode.VirtualSubNodeInputNodeFactory"/>
<entry key="node-name" type="xstring" value="Component Input"/>
<entry key="node-bundle-name" type="xstring" value="KNIME Core API"/>
<entry key="node-bundle-symbolic-name" type="xstring" value="org.knime.core"/>
<entry key="node-bundle-vendor" type="xstring" value="KNIME AG, Zurich, Switzerland"/>
<entry key="node-bundle-version" type="xstring" value="4.7.7.v202308161346"/>
<entry key="node-feature-name" type="xstring" value="KNIME AP Core feature"/>
<entry key="node-feature-symbolic-name" type="xstring" value="org.knime.features.core.feature.group"/>
<entry key="node-feature-vendor" type="xstring" value="KNIME AG, Zurich, Switzerland"/>
<entry key="node-feature-version" type="xstring" value="4.7.7.v202308161346"/>
<config key="factory_settings">
<config key="port_0">
<entry key="index" type="xint" value="0"/>
<config key="type">
<entry key="object_class" type="xstring" value="org.knime.core.node.BufferedDataTable"/>
</config>
</config>
</config>
<entry key="name" type="xstring" value="Component Input"/>
<entry key="hasContent" type="xboolean" value="false"/>
<entry key="isInactive" type="xboolean" value="false"/>
<config key="ports">
<config key="port_1">
<entry key="index" type="xint" value="1"/>
<entry key="port_dir_location" type="xstring" isnull="true" value=""/>
</config>
</config>
<config key="filestores">
<entry key="file_store_location" type="xstring" isnull="true" value=""/>
<entry key="file_store_id" type="xstring" isnull="true" value=""/>
</config>
</config>
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