| Previous changeset 15:97a7f34fcb6a (2021-08-11) Next changeset 17:1f39c833f65f (2022-07-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 80eb79844e82da22ce44a2ee9c9f202bed0b94d1 |
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modified:
macros.xml maxquant.xml |
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added:
README.rst |
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removed:
README.md |
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| diff -r 97a7f34fcb6a -r 74f5d355d156 README.md --- a/README.md Wed Aug 11 09:24:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,27 +0,0 @@ -GalaxyP - MaxQuant -================== - -* Home: <https://github.com/galaxyproteomics/tools-galaxyp/> -* Tool ID: `maxquant` -* Tool Type: `default` - - -Description ------------ - -Wrapper for the MaxQuant version available in conda. - - -Updating --------- - -MaxQuant often changes the layout of its parameters file. -So changes to the code are likely to be necessary when -updating to a new version of MaxQuant. The init.py script -can be used to initialize the tool with a new list of -modifications or enzymes. From the tool dir run: - -./init.py -m MODIFICATIONS.XML -e ENZYMES.XML - -The location of these xml files usually is: -ANACONDA_DIR/bin/conf/ \ No newline at end of file |
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| diff -r 97a7f34fcb6a -r 74f5d355d156 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Jul 22 07:10:28 2022 +0000 |
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| @@ -0,0 +1,27 @@ + +GalaxyP - MaxQuant +================== + + +* Home: https://github.com/galaxyproteomics/tools-galaxyp/ +* Tool ID: ``maxquant`` +* Tool Type: ``default`` + +Description +----------- + +Wrapper for the MaxQuant version available in conda. + +Updating +-------- + +MaxQuant often changes the layout of its parameters file. +So changes to the code are likely to be necessary when +updating to a new version of MaxQuant. The init.py script +can be used to initialize the tool with a new list of +modifications or enzymes. From the tool dir run: + +./init.py -m MODIFICATIONS.XML -e ENZYMES.XML + +The location of these xml files usually is: +ANACONDA_DIR/bin/conf/ |
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| diff -r 97a7f34fcb6a -r 74f5d355d156 macros.xml --- a/macros.xml Wed Aug 11 09:24:23 2021 +0000 +++ b/macros.xml Fri Jul 22 07:10:28 2022 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0" ?> <macros> <token name="@VERSION@">1.6.17.0</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX@">4</token> <token name="@VERSION_SUFFIX_MQPAR@">0</token> <token name="@VERSION_PTXQC@">1.0.10</token> <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token> @@ -255,9 +255,6 @@ </xml> <xml name="modification"> <expand macro="mod_option" value="Acetyl (K)"/> - <expand macro="mod_option" value="Acetyl (Protein N-term)"/> - <expand macro="mod_option" value="Carbamidomethyl (C)"/> - <expand macro="mod_option" value="Oxidation (M)"/> <expand macro="mod_option" value="Phospho (STY)"/> <expand macro="mod_option" value="GlyGly (K)"/> <expand macro="mod_option" value="Methyl (KR)"/> @@ -712,7 +709,6 @@ </xml> <xml name="proteases"> <expand macro="mod_option" value="Trypsin"/> - <expand macro="mod_option" value="Trypsin/P"/> <expand macro="mod_option" value="LysC"/> <expand macro="mod_option" value="LysC/P"/> <expand macro="mod_option" value="D.P"/> @@ -878,4 +874,4 @@ <citation type="doi">10.1021/acs.jproteome.5b00780</citation> </citations> </xml> -</macros> \ No newline at end of file +</macros> |
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| diff -r 97a7f34fcb6a -r 74f5d355d156 maxquant.xml --- a/maxquant.xml Wed Aug 11 09:24:23 2021 +0000 +++ b/maxquant.xml Fri Jul 22 07:10:28 2022 +0000 |
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| @@ -384,6 +384,7 @@ help="Peptides containing only these modifications will be used for the quantification of proteins in addition to unmodified peptides. This includes ratio and intensity calculations including iBAQ"> <expand macro="default_mod_option" value="Oxidation (M)"/> <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/> + <expand macro="mod_option" value="Carbamidomethyl (C)"/> <expand macro="modification"/> </param> <!-- note: the following default is different to the mquant default --> @@ -431,7 +432,7 @@ <repeat name="paramGroups" title="Parameter Group" min="1" default="1"> - <param type="data" format="thermo.raw,mzXML,mzML" name="files" label="Infiles" multiple="true" + <param type="data" format="thermo.raw,mzxml,mzml" name="files" label="Infiles" multiple="true" help="Only select infiles matching the filetype specified in the input options."/> <param type="integer" name="maxMissedCleavages" label="missed cleavages" value="2" @@ -439,14 +440,17 @@ <param name="fixedModifications" type="select" label="fixed modifications" multiple="true" help="Select zero or more fixed modifications. They will always be attached to any occurence of the respective amino acid."> + <expand macro="mod_option" value="Acetyl (Protein N-term)"/> + <expand macro="default_mod_option" value="Carbamidomethyl (C)"/> + <expand macro="mod_option" value="Oxidation (M)"/> <expand macro="modification"/> - <expand macro="default_mod_option" value="Carbamidomethyl (C)"/> </param> <param name="variableModifications" type="select" label="variable modifications" multiple="true" help="Select zero or more variable modifications. Do not specify label modifications here, neither ms1 level labels, like SILAC, nor isobaric labels."> + <expand macro="mod_option" value="Carbamidomethyl (C)"/> <expand macro="default_mod_option" value="Oxidation (M)"/> - <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/> + <expand macro="mod_option" value="Acetyl (Protein N-term)"/> <expand macro="modification"/> </param> <param name="enzymes" type="select" label="enzyme" @@ -1008,9 +1012,9 @@ **Input files** -- Thermo raw, mzML, mzXMLfiles (in parameter group section) +- Thermo raw, mzML, or mzXML files (in parameter group section) - - The datatype of all files has to be either 'thermo.raw', 'mzML' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes) + - The datatype of all files has to be either 'thermo.raw', 'mzml' or 'mzxml'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes) - Fasta file: specify parse rules according to your fasta file (header). Some examples for different fasta headers: :: |