changeset 0:ebbb18d665fd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/krona_text.xml	Thu Oct 08 11:21:08 2015 -0400
@@ -0,0 +1,49 @@
+<tool id="krona-text" name="Visualize  with Krona" version="1">
+
+  <description>Visualise any hierarchical data</description> 
+
+  <requirements>		
+    <requirement type="package" version="2.6">krona-tools</requirement>
+  </requirements>
+        
+  <!-- the command to run when user hits execute. Run our Rscript and pass the parameter to it -->
+  <command interpreter="bash">
+    runKrona.sh $inputfile $isMothur $outputfile
+
+
+  </command>
+
+
+  <inputs>
+  <!-- parameter examples, see https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax for descriptions -->
+
+    <!-- file from history -->
+    <param name="inputfile" type="data" label="Select input file" help="Choose input file from history. Format: count - Hierarchy (tab separated)"/>
+    <param name="isMothur" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="is this output from MOTHUR?" help="e.g. taxonomy file generated from Classify.seqs?"/>
+
+    
+  </inputs>
+
+  
+  <outputs>
+    <data format="html" name="outputfile"  from_work_dir="text.krona.html" label="Krona output: HTML"/>
+  </outputs>
+
+  <help>
+Input file must be a tab-delimited file with first column being a count, rest the hierarchy, for example::
+
+    2	Fats	Saturated fat  
+    3	Fats	Unsaturated fat	Monounsaturated fat  
+    3	Fats	Unsaturated fat	Polyunsaturated fat  
+    13	Carbohydrates	Sugars  
+    4	Carbohydrates	Dietary fiber  
+    21	Carbohydrates  
+    5	Protein  
+    4  
+
+Would yield the following graph: http://krona.sourceforge.net/examples/text.krona.html
+
+
+    
+  </help>
+</tool> 
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runKrona.sh	Thu Oct 08 11:21:08 2015 -0400
@@ -0,0 +1,29 @@
+# do krona visualisation
+#  runKrona.sh $infile $mothurtax $outputfile
+
+inputfile=$1
+isMothur=$2
+
+# preprocess if taxonomy from MOTHUR
+echo "starting"
+head $inputfile
+
+if [[ $isMothur == "Y" ]]
+then
+  awk 'BEGIN{FS="\t";OFS="\t"}{print $2,$3}' $inputfile > tempinput
+  head tempinput
+  sed -i 's/;/\t/g' tempinput
+  head tempinput
+ 
+else
+  cp $inputfile tempinput
+  
+fi
+
+head tempinput
+
+# run Krona
+echo $PATH
+ktImportText tempinput
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Oct 08 11:21:08 2015 -0400
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<tool_dependency>
+   <package name="krona-tools" version="2.6"> 
+        <install version="1.0">
+            <actions>                    
+                <action type="download_by_url">https://github.com/marbl/Krona/releases/download/v2.6/KronaTools-2.6.tar</action>
+                <action type="shell_command"> ./install.pl --prefix=.</action>
+                <action type="shell_command"> ls </action>
+                <action type="shell_command"> chmod a+x scripts/* </action>
+                <action type="shell_command"> cp -R * $INSTALL_DIR </action>                 
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
+                </action>
+                <action type="shell_command"> cd $INSTALL_DIR/scripts </action>
+                <action type="shell_command"> ls </action>
+                <action type="shell_command"> cd $INSTALL_DIR/scripts; for filename in *; do ln -s "$filename" "kt${filename%.pl}"; done;    </action>
+           </actions>
+        </install>
+        <readme>
+           Downloads and installs KronaTools. 
+        </readme>
+    </package>      
+</tool_dependency>
+