comparison pathwaymatcher.xml @ 2:03487adf8fc2 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9

1:ee1dfac35bb3

    <description>
        PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome.
    </description>
    <macros>
       <token name="@PATHWAYMATCHER_VERSION@">1.8.1</token>
       <token name="@TOOL_SUBVERSION@">0</token>
       <xml name="input_fasta">
         <param format="fasta" name="input_database" type="data" label="Protein Database"
             help="Select FASTA database from history"/>
       </xml>
    </macros>

The output of PathwayMatcher is composed of two files, the Reaction and Pathway mapping and the statistical analysis of the relevant pathways.

.. class:: infomark

Information included with this tool is a brief summary of the main one included in PathwayMatcher_.

Specific information about PathwayMatcher's Input_ and Output_ may also be found there.


.. class:: infomark

**References**

2:03487adf8fc2

    <description>
        PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome.
    </description>
    <macros>
       <token name="@PATHWAYMATCHER_VERSION@">1.8.1</token>
       <token name="@TOOL_SUBVERSION@">2</token>
       <xml name="input_fasta">
         <param format="fasta" name="input_database" type="data" label="Protein Database"
             help="Select FASTA database from history"/>
       </xml>
    </macros>

The output of PathwayMatcher is composed of two files, the Reaction and Pathway mapping and the statistical analysis of the relevant pathways.

.. class:: infomark

**Try it now**

You can easily test PathwayMatcher functionality using the example files we provide with proteoforms and proteins information of Cystic Fibrosis:

https://raw.githubusercontent.com/PathwayAnalysisPlatform/PathwayMatcher/master/resources/input/Proteoforms/Simple/CysticFibrosis.txt

https://raw.githubusercontent.com/PathwayAnalysisPlatform/PathwayMatcher/master/resources/input/Proteins/UniProt/CysticFibrosis.txt

You can upload them to Galaxy by directly copying and pasting their URL into the Galaxy upload dialog (the button with the arrow pointing up in the top-left area, and then choosing *Pasta/Fetch data*).

Once they appear in green in your history, they have been uploaded and you can use them as inputs in PathwayMatcher.

Now, select *Proteoforms* as input type and, in the next drop-down list, the entry of your history corresponding to the proteoforms file you uploaded.

Then, click on *insert input* to add a new PathwayMatcher input for the proteins. Select *Proteins - Uniprot accession list* as input type and, in the next drop-down list, the entry in your history corresponding to this proteins file.

**Everything is ready**. By clicking on *Execute* PathwayMatcher will run with your chosen inputs and, after a short time, it will show in your history two more files with the search results and its analysis.

.. class:: infomark

Information included with this tool is a brief summary of the main one included in PathwayMatcher_.

Specific information about PathwayMatcher's Input_ and Output_ may also be found there.

.. class:: infomark

**References**