comparison mqppep_preproc.xml @ 1:2ccb9727516b draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be

0:ba62d93a9ef5

                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=========================================================
Phopsphoproteomic Enrichment Pipeline Preprocessing Steps
=========================================================

**Overview**

Prior to statistical analysis, it is necessary to perform
three steps to transform the MaxQuant output
for phosphoproteome-enriched samples.

**Workflow position**

``upstream tool``
      The input data file for this tool is the ``Phospho (STY)Sites.txt`` file that is produced:

      - by the Galaxy "MaxQuant" (``maxquant``) tool
      - or by the Galaxy "Maxquant (using mqpar.xml)" (``maxquant_mqpar``) tool
      - or by the desktop version of MaxQuant.

``downstream tool``
  The "MaxQuant Phosphopeptide ANOVA" tool (``mqppep_anova``) consumes the ``merged/filtered`` output file ``preproc_tab`` that this tool produces.

======================================================================
Phopsphoproteomic Enrichment Pipeline Localization-Probability Cut-Off
======================================================================

This step applies a "localization-probability cut-off" for phosphopeptides for each phosphopeptide.
Higher values may reduce the number of peptides in the output.
The default value of 0.75 reflects the text of [Cheng  2018]:

[Bielow 2016] (available at `https://github.com/cbielow/PTXQC/
<https://github.com/cbielow/PTXQC/>`_) is run by the Galaxy wrappers for MaxQuant,
so it is omitted here even though it was included in Larry Cheng's original script.


**Input dataset**

``phosphoSites``
    This is the ``MaxQuant Phospho (STY)Sites.txt`` file produced by MaxQuant.
    If you use the desktop version of MaxQuant, you will find this file in the ``txt`` folder.

**Output datasets**

``ppep_intensities``
  Data table (in tabular format) presenting, for each sample, the mass-spectral intensity of each phopshopeptide having localization probability greater than the cutoff.
``enrichment.pdf``
  Graph (in PDF format) presenting non-zero proportions of pS, pT, and pY among the phosphosites; note that a phosphopeptide may have multiple phosphosite.
``locProbCutoff.pdf``
  Graph (in PDF format) contrasting proportion of phosphopeptides above the localization probability cutoff with the proportion below.
``enrichment.svg``
  Enrichment graph (in downloadable "scalable vector graphics" format) for incorporation into documents.
``locProbCutoff.svg``
  Localization probability cutoff graph (in downloadable "scalable vector graphics" format) for incorporation into documents.
``filteredData``
  Data table (in tabular format) comprising rows of the ``phosphSites`` input file that are not flagged as contaminants or reversed sequences.
``quantData``
  Data table (in tabular format) comprising rows of the ``filteredData`` file whose localization probability exceeds the **Localization Probability Cutoff** parameter.

**Authors**

``Nicholas A. Graham``
  (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script.

``Larry C. Cheng``

``James E. Johnson``
  (University of Minnesota Supercomputing Institute) adapted the script to run in Galaxy.


=============================================================
Phopsphoproteomic Enrichment Pipeline Upstream Kinase Mapping
=============================================================

This step searches phosphopeptides against several databases for known or predicted sites.

**Input databases**

``networkin``
    This table is the result of filtering the NetworkKIN database [Linding 2007; Horn 2014] for cutoff score > 2.0.  The ENSEMBL data used to generate the file were from Ensembl, `ensembl.org <https://web.archive.org/web/20220308011159/http://useast.ensembl.org/index.html>`_ [Howe 2021].

       *To generate this file:*

       **(1)** Download the "precomputed data for all available kinase predictors against ENSEMBL"
       (Available at the NetworkKIN predictions link on the downloads page at https://web.archive.org/web/20200208000403/http://networkin.info/download/networkin_human_predictions_3.1.tsv.xz;  N.B.: "Commercial users are requested to contact the authors before using the data on the networkin.info website");

       **(2)** Decompress the .tsv.xz with file with "unxz" (from XZ Utils `https://tukaani.org/xz/ <https://tukaani.org/xz/>`_);

       **(3)** Filter out the rows having "network_kin" less than 2.0.

       The result should be a tab-separated file with the following columns:

           1. ``#substrate``
           2. ``position``
           3. ``id``
           4. ``networkin_score``
           5. ``tree``
           6. ``netphorest_group``
           7. ``netphorest_score``
           8. ``string_identifier``
           9. ``string_score``
           10. ``substrate_name``
           11. ``sequence``
           12. ``string_path``


``p_sty_motifs``
  This database merges motif patterns from [Amanchy 2007] and Phosida [Gnad 2011].

    The Amanchy data are adapted from `http://hprd.org/serine_motifs <http://hprd.org/serine_motifs>`_ and `http://hprd.org/tyrosine_motifs <http://hprd.org/tyrosine_motifs>`_ (both links cite the reference where each motif was published), and the patterns are translated into Perl regular expression format (`https://perldoc.perl.org/perlre <https://perldoc.perl.org/perlre>`_).

    The Phosida data are adapted (translated to Perl-formatted regular expressions) from `http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx <http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx>`_ (this link cites the reference where each motif was published).

      This file has three tab-separated columns (and no header):

         1. column 1 is an (ignored) identifier
         2. column 2 is a Perl regular expression
         3. column 3 is a descriptor.

      For two examples:

      ``2<TAB>R.R..(pS|pT)<TAB>Akt kinase substrate motif (HPRD)``

      ``10<TAB>R..(pS|pT)V<TAB>CAMK2_Phosida``

``psp_kinase_substrate``
  'Kinase-substrate dataset: experimentally determined substrates, sequences, cognate kinases, and metadata curated from the literature' [Hornbeck 2011].  This tabular-formatted file may be downloaded for non-commercial purposes as 'Kinase_Substrate_Dataset.gz' from `https://www.phosphosite.org/staticDownloads.action <https://www.phosphosite.org/staticDownloads.action>`_.

      Data extracted from PhosphoSitePlus(R), created by Cell Signaling Technology Inc. PhosphoSitePlus is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License (`https://creativecommons.org/licenses/by-nc-sa/3.0/ <https://creativecommons.org/licenses/by-nc-sa/3.0/>`_). Attribution must be given in written, oral and digital presentations to PhosphoSitePlus, www.phosphosite.org. Written documents should additionally cite:

          Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40, D261-D270.; www.phosphosite.org.

``psp_regulatory_sites``
  'Regulatory sites: information curated from the literature about modification sites shown to regulate molecular functions, biological processes, and molecular interactions including protein-protein interactions' [Hornbeck 2011].  This tabular-formatted file may be downloaded for non-commercial purposes as 'Regulatory_sites.gz' from `https://www.phosphosite.org/staticDownloads.action <https://www.phosphosite.org/staticDownloads.action>`_.

      Terms of use and citatation are as for the ``psp_kinase_substrate`` file.

**Output datasets**

``ppep_map``
  Data table (in tabular format, consumed by the merge/filter step) presenting, for each phosphopeptide, the kinase mappings,  the mass-spectral intensities for each sample, and the metadata from UniProtKB/SwissProt, phospho-sites, phospho-motifs, and regulatory sites.  Data in the columns marked "``Domain``", "``ON_...``", or "``..._PhosphoSite``" are available subject to the following terms:

    "PhosphoSitePlus\ |reg| (PSP) was created by Cell Signaling Technology Inc. It is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License(`https://creativecommons.org/licenses/by-nc-sa/3.0/ <https://creativecommons.org/licenses/by-nc-sa/3.0/>`_). When using PSP data or analyses in printed publications or in online resources, the following acknowledgements must be included: (a) the words 'PhosphoSitePlus(R), www.phosphosite.org' must be included at appropriate places in the text or webpage, and (b) citation of [Hornbeck 2011 (`PMID: 25514926 <https://pubmed.ncbi.nlm.nih.gov/25514926>`_)] must be included in the bibliography."

  Data table (in tabular format) presenting, for each phosphopeptide, the gene and one of the phospho-motifs or kinase-substrate sites.

``ppep_mapping_sqlite``
  SQLite database (consumed by the merge/filter step).

**Authors**

``Nicholas A. Graham``
  (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) wrote the original script.

``Arthur C. Eschenlauer``
  (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.


======================================================
Phopsphoproteomic Enrichment Pipeline Merge and Filter
======================================================

This step merges mapped metadata into metadata for phosphopeptides, filtering by species.

**Input parameters**

``species``
  Limit PhosphoSitesPlus to indicated species. Default: **human**

**Output datasets**

``preproc_tab``
  Phosphopeptides annotated with SwissProt and phosphosite metadata, in tabular format.  This file is designed to be consumed by the downstream ANOVA tool.  Some data in the columns marked "PSP" are available subject to the following terms:

    "PhosphoSitePlus\ |reg| (PSP) was created by Cell Signaling Technology Inc. It is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License(`https://creativecommons.org/licenses/by-nc-sa/3.0/ <https://creativecommons.org/licenses/by-nc-sa/3.0/>`_). When using PSP data or analyses in printed publications or in online resources, the following acknowledgements must be included: (a) the words 'PhosphoSitePlus(R), www.phosphosite.org' must be included at appropriate places in the text or webpage, and (b) citation of [Hornbeck 2011 (`PMID: 25514926 <https://pubmed.ncbi.nlm.nih.gov/25514926>`_)] must be included in the bibliography."

  Phosphopeptides annotated with SwissProt and phosphosite metadata, in CSV format.

``preproc_sqlite``
  ``ppep_mapping_sqlite`` updated with annotations, in SQLite format.

**Authors**

``Nicholas A. Graham``
  (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script.

``Larry C. Cheng``

1:2ccb9727516b

                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=============================================================
**Phopsphoproteomic Enrichment Pipeline Preprocessing Steps**
=============================================================

*Overview*
==========

Prior to statistical analysis, it is necessary to perform
three steps to transform the MaxQuant output
for phosphoproteome-enriched samples.

*Workflow position*
===================

Upstream tool
=============

The input dataset for this tool is the ``Phospho (STY)Sites.txt`` file that is produced:

   - by the Galaxy "MaxQuant" (``maxquant``) tool
   - or by the Galaxy "Maxquant (using mqpar.xml)" (``maxquant_mqpar``) tool
   - or by the desktop version of MaxQuant.

Downstream tool
===============

The "MaxQuant Phosphopeptide ANOVA" tool (``mqppep_anova``) consumes the "preprocessed" output file ``preproc_tab`` that this tool produces.

*Phopsphoproteomic Enrichment Pipeline Localization-Probability Cut-Off*
========================================================================

This step applies a "localization-probability cut-off" for phosphopeptides for each phosphopeptide.
Higher values may reduce the number of peptides in the output.
The default value of 0.75 reflects the text of [Cheng  2018]:

[Bielow 2016] (available at `https://github.com/cbielow/PTXQC/
<https://github.com/cbielow/PTXQC/>`_) is run by the Galaxy wrappers for MaxQuant,
so it is omitted here even though it was included in Larry Cheng's original script.


Input dataset
=============

Phospho (STY)Sites.txt
   This is the ``MaxQuant Phospho (STY)Sites.txt`` file produced by MaxQuant.
   If you use the desktop version of MaxQuant, you will find this file in the ``txt`` folder.

Input parameters
================

Localization probability cutoff
  Minimum localization probability; see above.

Intensity merge-function
  Specifies how intensities for identical phosphosites should be merged; see above.

Output datasets
===============

``ppep_intensities``
  Data table (in tabular format) presenting, for each sample, the mass-spectral intensity of each phopshopeptide having localization probability greater than the cutoff.

``enrichment.pdf``
  Graph (in PDF format) presenting non-zero proportions of pS, pT, and pY among the phosphosites; note that a phosphopeptide may have multiple phosphosite.

``locProbCutoff.pdf``
  Graph (in PDF format) contrasting proportion of phosphopeptides above the localization probability cutoff with the proportion below.

``enrichment.svg``
  Enrichment graph (in downloadable "scalable vector graphics" format) for incorporation into documents.

``locProbCutoff.svg``
  Localization probability cutoff graph (in downloadable "scalable vector graphics" format) for incorporation into documents.

``filteredData``
  Data table (in tabular format) comprising rows of the ``phosphSites`` input file that are not flagged as contaminants or reversed sequences.

``quantData``
  Data table (in tabular format) comprising rows of the ``filteredData`` file whose localization probability exceeds the **Localization Probability Cutoff** parameter.

Authors
=======

``Nicholas A. Graham``
  (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script.

``Larry C. Cheng``

``James E. Johnson``
  (University of Minnesota Supercomputing Institute) adapted the script to run in Galaxy.


*Phopsphoproteomic Enrichment Pipeline Upstream Kinase Mapping*
===============================================================

This step searches phosphopeptides against several databases for known or predicted sites.

Input databases
===============

``networkin``
    This table is the result of filtering the NetworkKIN database [Linding 2007; Horn 2014] for cutoff score > 2.0.  The ENSEMBL data used to generate the file were from Ensembl, `ensembl.org <https://web.archive.org/web/20220308011159/http://useast.ensembl.org/index.html>`_ [Howe 2021].

To generate this file:

   (1) Download the "precomputed data for all available kinase predictors against ENSEMBL" (available at the NetworkKIN predictions link on the downloads page at https://web.archive.org/web/20200208000403/http://networkin.info/download/networkin_human_predictions_3.1.tsv.xz;  N.B.: "Commercial users are requested to contact the authors before using the data on the networkin.info website");
   (2) Decompress the .tsv.xz with file with "unxz" (from XZ Utils `https://tukaani.org/xz/ <https://tukaani.org/xz/>`_);
   (3) Filter out the rows having "network_kin" less than 2.0.

The result should be a tab-separated file with the following columns:

   - ``#substrate``
   - ``position``
   - ``id``
   - ``networkin_score``
   - ``tree``
   - ``netphorest_group``
   - ``netphorest_score``
   - ``string_identifier``
   - ``string_score``
   - ``substrate_name``
   - ``sequence``
   - ``string_path``


``p_sty_motifs``
   This database merges motif patterns from [Amanchy 2007] and Phosida [Gnad 2011].

     The Amanchy data are adapted from `https://web.archive.org/web/*/http://hprd.org/serine_motifs <https://web.archive.org/web/*/http://hprd.org/serine_motifs>`_ and `https://web.archive.org/web/*/http://hprd.org/tyrosine_motifs <https://web.archive.org/web/*/http://hprd.org/tyrosine_motifs>`_ (both links cite the reference where each motif was published), and the patterns are translated into Perl regular expression format (`https://perldoc.perl.org/perlre <https://perldoc.perl.org/perlre>`_).

   The Phosida data are adapted (translated to Perl-formatted regular expressions) from `http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx <http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx>`_ (this link cites the reference where each motif was published).

   This file has three tab-separated columns (and no header):

      - column 1 is an (ignored) identifier
      - column 2 is a Perl regular expression
      - column 3 is a descriptor.

   For two examples:

       ``2<TAB>R.R..(pS|pT)<TAB>Akt kinase substrate motif (HPRD)``

       ``10<TAB>R..(pS|pT)V<TAB>CAMK2_Phosida``

``psp_kinase_substrate``
   'Kinase-substrate dataset: experimentally determined substrates, sequences, cognate kinases, and metadata curated from the literature' [Hornbeck 2011].  This tabular-formatted file may be downloaded for non-commercial purposes as 'Kinase_Substrate_Dataset.gz' from `https://www.phosphosite.org/staticDownloads.action <https://www.phosphosite.org/staticDownloads.action>`_.

       Data extracted from PhosphoSitePlus(R), created by Cell Signaling Technology Inc. PhosphoSitePlus is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License (`https://creativecommons.org/licenses/by-nc-sa/3.0/ <https://creativecommons.org/licenses/by-nc-sa/3.0/>`_). Attribution must be given in written, oral and digital presentations to PhosphoSitePlus, www.phosphosite.org. Written documents should additionally cite:

       Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40, D261-D270.; www.phosphosite.org.

``psp_regulatory_sites``
   'Regulatory sites: information curated from the literature about modification sites shown to regulate molecular functions, biological processes, and molecular interactions including protein-protein interactions' [Hornbeck 2011].  This tabular-formatted file may be downloaded for non-commercial purposes as 'Regulatory_sites.gz' from `https://www.phosphosite.org/staticDownloads.action <https://www.phosphosite.org/staticDownloads.action>`_.

      Terms of use and citatation are as for the ``psp_kinase_substrate`` file.

Output datasets
===============

``ppep_map``
  Data table (in tabular format, consumed by the merge/filter step) presenting, for each phosphopeptide, the kinase mappings,  the mass-spectral intensities for each sample, and the metadata from UniProtKB/SwissProt, phospho-sites, phospho-motifs, and regulatory sites.  Data in the columns marked "``Domain``", "``ON_...``", or "``..._PhosphoSite``" are available subject to the following terms:

    "PhosphoSitePlus\ |reg| (PSP) was created by Cell Signaling Technology Inc. It is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License(`https://creativecommons.org/licenses/by-nc-sa/3.0/ <https://creativecommons.org/licenses/by-nc-sa/3.0/>`_). When using PSP data or analyses in printed publications or in online resources, the following acknowledgements must be included: (a) the words 'PhosphoSitePlus(R), www.phosphosite.org' must be included at appropriate places in the text or webpage, and (b) citation of [Hornbeck 2011 (`PMID: 25514926 <https://pubmed.ncbi.nlm.nih.gov/25514926>`_)] must be included in the bibliography."

  Data table (in tabular format) presenting, for each phosphopeptide, the gene and one of the phospho-motifs or kinase-substrate sites.

``ppep_mapping_sqlite``
  SQLite database (consumed by the merge/filter step).

Authors
=======

``Nicholas A. Graham``
  (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) wrote the original script.

``Arthur C. Eschenlauer``
  (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.


*Phopsphoproteomic Enrichment Pipeline Merge and Filter*
========================================================

This step merges mapped metadata into metadata for phosphopeptides, filtering by species.

Input parameters
================

``species``
  Limit PhosphoSitesPlus to indicated species. Default: **human**

Output datasets
===============

``preproc_tab``
  Phosphopeptides annotated with SwissProt and phosphosite metadata, in tabular format.  This file is designed to be consumed by the downstream ANOVA tool.  Some data in the columns marked "PSP" are available subject to the following terms:

    "PhosphoSitePlus\ |reg| (PSP) was created by Cell Signaling Technology Inc. It is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License(`https://creativecommons.org/licenses/by-nc-sa/3.0/ <https://creativecommons.org/licenses/by-nc-sa/3.0/>`_). When using PSP data or analyses in printed publications or in online resources, the following acknowledgements must be included: (a) the words 'PhosphoSitePlus(R), www.phosphosite.org' must be included at appropriate places in the text or webpage, and (b) citation of [Hornbeck 2011 (`PMID: 25514926 <https://pubmed.ncbi.nlm.nih.gov/25514926>`_)] must be included in the bibliography."

  Phosphopeptides annotated with SwissProt and phosphosite metadata, in CSV format.

``preproc_sqlite``
  ``ppep_mapping_sqlite`` updated with annotations, in SQLite format.

Authors
=======

``Nicholas A. Graham``
  (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script.

``Larry C. Cheng``