Mercurial > repos > galaxyp > reactome_pathwaymatcher
changeset 2:03487adf8fc2 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
| author | galaxyp |
|---|---|
| date | Thu, 26 Jul 2018 17:00:22 -0400 |
| parents | ee1dfac35bb3 |
| children | f3be3f08dcfa |
| files | README.rst pathwaymatcher.xml |
| diffstat | 2 files changed, 24 insertions(+), 5 deletions(-) [+] |
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--- 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
--- 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**