comparison maxquant.xml @ 16:74f5d355d156 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 80eb79844e82da22ce44a2ee9c9f202bed0b94d1

15:97a7f34fcb6a

                    <param name="mods_used_prot_quant" type="select" multiple="true"
                           label="Modifications used in protein quantification"
                           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="modification"/>
                    </param>
                    <!-- note: the following default is different to the mquant default -->
                    <param name="discard_unmod_cpart_peptides" type="boolean" label="Discard unmodified counterpart peptides" checked="true"
                           truevalue="True" falsevalue="False"

        </section>


        <repeat name="paramGroups" title="Parameter Group" min="1" default="1">
            <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"
                   help="The number of missed cleavages that are maximally tolerated in the in-silico digestion of the protien sequences."/>
            <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="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="default_mod_option" value="Oxidation (M)"/>
                <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/>
                <expand macro="modification"/>
            </param>
            <param name="enzymes" type="select" label="enzyme"
                   multiple="true"
                   help="Select zero or more enzymes. The enzymes used for generating the in silico peptides for the Andromeda search.">

This tool is a wrapper for MaxQuant v@VERSION@. The current version of the wrapper only supports a reduced set of parameters, but another version of the tool that gets its parameters directly from a mqpar.xml file is available, too.

**Input files**

- Thermo raw, mzML, mzXMLfiles (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)
- Fasta file: specify parse rules according to your fasta file (header). Some examples for different fasta headers:  

                ::

                                            identifier parse rule     description parse rule

16:74f5d355d156

                    <param name="mods_used_prot_quant" type="select" multiple="true"
                           label="Modifications used in protein quantification"
                           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 -->
                    <param name="discard_unmod_cpart_peptides" type="boolean" label="Discard unmodified counterpart peptides" checked="true"
                           truevalue="True" falsevalue="False"

        </section>


        <repeat name="paramGroups" title="Parameter Group" min="1" default="1">
            <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"
                   help="The number of missed cleavages that are maximally tolerated in the in-silico digestion of the protien sequences."/>
            <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"/>
            </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="mod_option" value="Acetyl (Protein N-term)"/>
                <expand macro="modification"/>
            </param>
            <param name="enzymes" type="select" label="enzyme"
                   multiple="true"
                   help="Select zero or more enzymes. The enzymes used for generating the in silico peptides for the Andromeda search.">

This tool is a wrapper for MaxQuant v@VERSION@. The current version of the wrapper only supports a reduced set of parameters, but another version of the tool that gets its parameters directly from a mqpar.xml file is available, too.

**Input files**

- 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)
- Fasta file: specify parse rules according to your fasta file (header). Some examples for different fasta headers:  

                ::

                                            identifier parse rule     description parse rule