# HG changeset patch
# User petr-novak
# Date 1709543794 0
# Node ID 04021cfd51701253c9856080d6df1e53aadfa617

planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 5269b4297ea690bce0802c3c1cb217f24290f1ec-dirty

diff -r 000000000000 -r 04021cfd5170 README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Mon Mar 04 09:16:34 2024 +0000
@@ -0,0 +1,14 @@
+Krona visualistion on generic hierarchy files.
+
+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
\ No newline at end of file
diff -r 000000000000 -r 04021cfd5170 krona_text.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/krona_text.xml	Mon Mar 04 09:16:34 2024 +0000
@@ -0,0 +1,58 @@
+<tool id="krona-text" name="Visualize  with Krona" version="1.1">
+
+  <description>Visualise any hierarchical data</description>
+
+  <requirements>
+    <requirement type="package" version="2.6">krona</requirement>
+  </requirements>
+  <command><![CDATA[
+echo "starting" &&
+head '${inputfile}' &&
+
+#if "$isMothur" == "Y"
+  awk 'BEGIN{FS="\t";OFS="\t"}{print $2,$3}' '${inputfile}' > tempinput &&
+  head tempinput &&
+  sed -i 's/;/\t/g' tempinput &&
+
+#else
+  cp '${inputfile}' tempinput &&
+
+#end if
+
+head tempinput &&
+export TERM=dumb &&
+ktImportText tempinput
+]]></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.otu?"/>
+
+
+  </inputs>
+
+
+  <outputs>
+    <data format="html" name="outputfile"  from_work_dir="text.krona.html" label="Krona on ${on_string}: 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
+This tool is a modification of https://toolshed.g2.bx.psu.edu/view/saskia-hiltemann/krona_text/b14f1444e464
+  </help>
+</tool>