# HG changeset patch # User ngsplot # Date 1426800460 14400 # Node ID bb51014370e1c5c87888aa7c21b10a84651d8bca # Parent c3c019ccc5b00b61679b62053033d895ed0aa623 Uploaded diff -r c3c019ccc5b0 -r bb51014370e1 ngsplot_galaxytoolshed_v1.0/ngsplot_intro/intro.xml --- a/ngsplot_galaxytoolshed_v1.0/ngsplot_intro/intro.xml Thu Mar 19 17:21:56 2015 -0400 +++ b/ngsplot_galaxytoolshed_v1.0/ngsplot_intro/intro.xml Thu Mar 19 17:27:40 2015 -0400 @@ -18,10 +18,12 @@ **HOW TO USE** -To use ngs.plot here on this GUI-based galaxy implementation, first upload your alignment BAM file(s) using the *Get Data* -> **Upload File** tool on top of the left panel of this page. The names of your uploaded file(s) will then be displayed on the right panel. Next, select the *NGS.PLOT V2.47.1* -> **ngs.plot** tool on the left panel and all other input information required from you will be displayed as a form on the main central panel. Complete the form then click the *Execute* button to launch the program. Three output files (a profile chart, a heatmap, and a zipped data file) will be generated and displayed on the right panel, which you can click on to view. To further replot the figures into a format that you desire, use the *NGS.PLOT V2.47.1* -> **replot** tool with it's input file being the zip file previously generated by 'ngs.plot'. +To use ngs.plot here on this GUI-based Galaxy implementation, first upload your alignment BAM file(s) using the *Get Data* -> **Upload File** tool on top of the left panel of this page. The names of your uploaded file(s) will then be displayed on the right panel. Next, select the *NGS.PLOT V2.47.1* -> **ngs.plot** tool on the left panel and all other input information required from you will be displayed as a form on the main central panel. Complete the form then click the *Execute* button to launch the program. Three output files (a profile chart, a heatmap, and a zipped data file) will be generated and displayed on the right panel, which you can click on to view. To further replot the figures into a format that you desire, use the *NGS.PLOT V2.47.1* -> **replot** tool with it's input file being the zip file previously generated by 'ngs.plot'. For a more detailed explanation of how to run ngs.plot on Galaxy, please see the tutorial at https://code.google.com/p/ngsplot/wiki/webngsplot. +(Note: installation of this Galaxy implementation of ngs.plot directly from the Galaxy Toolshed requires ngs.plot v2.47.1 to be already installed on your system. For instructions on the system installation of ngs.plot, please see https://code.google.com/p/ngsplot/. + ----- **INTRODUCTION** @@ -48,9 +50,6 @@ ----- -**Galaxy Toolshed Installation** - -Please note that the Galaxy Toolshed implementation of ngs.plot requires ngs.plot v2.47.1 to be already installed on your system. For instructions on the system installation of ngs.plot, please see https://code.google.com/p/ngsplot/.