annotate workflow/ppenrich_suite_wf.ga @ 5:514afed1f40d draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aa5f4a19e76ec636812865293b8ee9b196122121

{
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    "annotation": "phoshpoproteomic enrichment data pre-processing and ANOVA",
    "creator": [
        {
            "class": "Person",
            "identifier": "0000-0002-2882-0508",
            "name": "Art Eschenlauer"
        }
    ],
    "format-version": "0.1",
    "license": "MIT",
    "name": "ppenrich_suite_wf",
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            "annotation": "The Phospho (STY)Sites.txt file produced by MaxQuant (found in the txt folder).",
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                {
                    "description": "The Phospho (STY)Sites.txt file produced by MaxQuant (found in the txt folder).",
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                {
                    "description": "THIS IS pST BY DEFAULT.  Change if your data are enriched for pY.",
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            "annotation": "Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)",
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                {
                    "description": "Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)",
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            "label": "Intensity-column pattern",
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                    "description": "Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)",
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            "label": "Sample-extraction pattern",
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            "annotation": "Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)",
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            "inputs": [
                {
                    "description": "Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)",
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            "label": "Group-extraction pattern",
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                    "description": "FASTA file of all human canonical isoforms, derived from Swiss-Prot (e.g., merge of https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot_varsplic.fasta.gz and https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz)",
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            "label": "SwissProt_Human_Canonical_Isoform.fasta",
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            "uuid": "870d3075-3ebb-4505-99a2-c3d01b51a86b",
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        "6": {
            "annotation": "Derived from https://networkin.info/download/networkin_human_predictions_3.1.tsv.xz (which is free for non-commercial use - for required citation, see https://networkin.info/)",
            "content_id": null,
            "errors": null,
            "id": 6,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Derived from https://networkin.info/download/networkin_human_predictions_3.1.tsv.xz (which is free for non-commercial use - for required citation, see https://networkin.info/)",
                    "name": "NetworKIN_cutoffscore2.0.tabular"
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            ],
            "label": "NetworKIN_cutoffscore2.0.tabular",
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            "annotation": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx",
            "content_id": null,
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                    "description": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx",
                    "name": "pSTY_Motifs.tabular"
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            "label": "pSTY_Motifs.tabular",
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        "8": {
            "annotation": "Derived from Kinase_Substrate_Dataset.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use  - see that link for citation.)",
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                {
                    "description": "Derived from Kinase_Substrate_Dataset.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use  - see that link for citation.)",
                    "name": "PSP_Kinase_Substrate_Dataset.tabular"
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            ],
            "label": "PSP_Kinase_Substrate_Dataset.tabular",
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            "uuid": "ed06b46c-d6b3-4d52-a6e6-fa5211da5a0a",
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            "annotation": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use  - see that link for citation.)",
            "content_id": null,
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            "id": 9,
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            "inputs": [
                {
                    "description": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use  - see that link for citation.)",
                    "name": "PSP_Regulatory_sites.tabular"
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            ],
            "label": "PSP_Regulatory_sites.tabular",
            "name": "Input dataset",
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            "annotation": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.",
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                {
                    "description": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.",
                    "name": "alpha_levels.tabular"
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            "label": "alpha_levels.tabular",
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            "annotation": "Transform the output of MaxQuant for phosphoproteome-enriched samples to prepare it for statistical anlaysis.",
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                    "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing",
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                {
                    "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing",
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                    "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing",
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                {
                    "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing",
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                {
                    "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing",
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                    "description": "runtime parameter for tool MaxQuant Phosphopeptide Preprocessing",
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            "label": "Preprocess MaxQuant Phospho (STY)Sites",
            "name": "MaxQuant Phosphopeptide Preprocessing",
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