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comparison msstatstmt.xml @ 6:bd1535813cfe draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 86de2cd327423c44d042f98108dc93a8f83982d0
author galaxyp
date Tue, 31 Jan 2023 18:15:05 +0000
parents a5e394b36d87
children
comparison
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5:a5e394b36d87 6:bd1535813cfe
1 <tool id="msstatstmt" name="MSstatsTMT" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="msstatstmt" name="MSstatsTMT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</description> 2 <description>protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.0.0</token> 4 <token name="@TOOL_VERSION@">2.0.0</token>
5 <token name="@GALAXY_VERSION@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 <xml name="input_options_shared"> 6 <xml name="input_options_shared">
7 <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use unique peptide" help="Yes (default) removes peptides that are assigned for more than one protein. We assume to use unique peptide for each protein." /> 7 <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use unique peptide" help="Yes (default) removes peptides that are assigned for more than one protein. We assume to use unique peptide for each protein." />
8 <param name="rmPSM_withMissing_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove PSM with missing value within run" help="Yes will remove PSM with any missing value within each run. Default is No." /> 8 <param name="rmPSM_withMissing_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove PSM with missing value within run" help="Yes will remove PSM with any missing value within each run. Default is No." />
9 <param name="rmPSM_withfewMea_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove PSM with few measurements within run" help="Only for 'Remove PSM with missing value within run = No'. Yes (default) will remove the features that have 1 or 2 measurements within each run." /> 9 <param name="rmPSM_withfewMea_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove PSM with few measurements within run" help="Only for 'Remove PSM with missing value within run = No'. Yes (default) will remove the features that have 1 or 2 measurements within each run." />
10 <param name="rmProtein_with1Feature" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove proteins with one feature" help="Yes will remove the proteins which have only 1 peptide and charge. Default is No." /> 10 <param name="rmProtein_with1Feature" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove proteins with one feature" help="Yes will remove the proteins which have only 1 peptide and charge. Default is No." />
620 ]]> 620 ]]>
621 </help> 621 </help>
622 622
623 <citations> 623 <citations>
624 <citation type="doi">10.1074/mcp.ra120.002105</citation> 624 <citation type="doi">10.1074/mcp.ra120.002105</citation>
625 <citation type="doi">10.1021/acs.jproteome.2c00051</citation>
625 </citations> 626 </citations>
626 </tool> 627 </tool>