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comparison msstats.xml @ 7:de7593c29499 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 63cff07026599f16d57da27c5897b7e88ad41ae5
author galaxyp
date Tue, 12 Mar 2024 11:46:51 +0000
parents b7034eff0db1
children
comparison
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6:b7034eff0db1 7:de7593c29499
21 <xml name="removeProtein_with1Peptide"> 21 <xml name="removeProtein_with1Peptide">
22 <param name="removeProtein_with1Peptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the proteins which have only 1 peptide and charge"/> 22 <param name="removeProtein_with1Peptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the proteins which have only 1 peptide and charge"/>
23 </xml> 23 </xml>
24 24
25 </macros> 25 </macros>
26 <xrefs>
27 <xref type="bio.tools">msstatstmt</xref>
28 </xrefs>
26 <requirements> 29 <requirements>
27 <requirement type="package" version="@TOOL_VERSION@">bioconductor-msstats</requirement> 30 <requirement type="package" version="@TOOL_VERSION@">bioconductor-msstats</requirement>
28 </requirements> 31 </requirements>
29 <command detect_errors="exit_code"><![CDATA[ 32 <command detect_errors="exit_code"><![CDATA[
30 cat '$msstats_script' > '$r_script' && 33 cat '$msstats_script' > '$r_script' &&
1018 1021
1019 ----- 1022 -----
1020 1023
1021 **Input data** 1024 **Input data**
1022 1025
1023 - Data in tabular or csv format, either in the 10-column MSstats format or the outputs of spectral processing tools such as `MaxQuant <http://coxdocs.org/doku.php?id=maxquant:start/>`_, `OpenSWATH <http://openswath.org/en/latest/>`_ 1026 - Data in tabular or csv format, either in the 10-column MSstats format or the outputs of spectral processing tools such as `MaxQuant <https://cox-labs.github.io/coxdocs/maxquant_instructions.html>`_, `OpenSWATH <http://openswath.org/en/latest/>`_
1024 1027
1025 - MSstats format: tabular file with 10 column either manually curated or other sources such as Swath2stats tool which is implemented in Pyprophet export in Galaxy. For manual curation: Names of headers are fixed but not case sensitive: 1028 - MSstats format: tabular file with 10 column either manually curated or other sources such as Swath2stats tool which is implemented in Pyprophet export in Galaxy. For manual curation: Names of headers are fixed but not case sensitive:
1026 1029
1027 - ProteinName: protein ID or peptide ID for peptide-level modeling and analysis; statistical analysis will be done separately for each unique label in this column 1030 - ProteinName: protein ID or peptide ID for peptide-level modeling and analysis; statistical analysis will be done separately for each unique label in this column
1028 - PeptideSequence: Amino acid sequence for each peptide. If the peptide sequences should be distinguished based on post-translational modifications, this column can be renamed to PeptideModifiedSequence. 1031 - PeptideSequence: Amino acid sequence for each peptide. If the peptide sequences should be distinguished based on post-translational modifications, this column can be renamed to PeptideModifiedSequence.