# HG changeset patch
# User galaxyp
# Date 1532638822 14400
# Node ID 03487adf8fc2c088c6db14c26881e3451128893b
# Parent  ee1dfac35bb318e93d6a39222cf178411eefcf70
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9

diff -r ee1dfac35bb3 -r 03487adf8fc2 README.rst
--- a/README.rst	Wed Jul 04 04:27:50 2018 -0400
+++ b/README.rst	Thu Jul 26 17:00:22 2018 -0400
@@ -1,9 +1,9 @@
 PathwayMatcher
 =======================
 
-- Home: <https://github.com/LuisFranciscoHS/PathwayMatcher/>
-- Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/pathwaymatcher>
-- Tools ID: `pathwaymatcher`
+- Home: <https://github.com/PathwayAnalysisPlatform/PathwayMatcher>
+- Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/reactome_pathwaymatcher>
+- Tools ID: `reactome_pathwaymatcher`
 
 
 Description
diff -r ee1dfac35bb3 -r 03487adf8fc2 pathwaymatcher.xml
--- a/pathwaymatcher.xml	Wed Jul 04 04:27:50 2018 -0400
+++ b/pathwaymatcher.xml	Thu Jul 26 17:00:22 2018 -0400
@@ -4,7 +4,7 @@
     </description>
     <macros>
        <token name="@PATHWAYMATCHER_VERSION@">1.8.1</token>
-       <token name="@TOOL_SUBVERSION@">0</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"/>
@@ -345,11 +345,30 @@
 
 .. 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**