# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1351536767 18000
# Node ID 53258f6dddd36ebedb9844b379ac23f25c90c38b
# Parent  f8fdde273a2a05c4b4f751af38fe0b2fbb7adab9
Add tool_dependencies.xml

diff -r f8fdde273a2a -r 53258f6dddd3 classify_blast.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/classify_blast.xml	Mon Oct 29 13:52:47 2012 -0500
@@ -0,0 +1,75 @@
+<tool id="classify_blast" name="Classify BLAST" version="1.0.0">
+<description>results using KronaTools</description>
+<command>
+	ktClassifyBLAST
+	-o $output
+	-e $factor
+	$random
+	#if $score == 'percentIdentity':
+		-p
+	#elif $score == 'bitScore':
+		-b
+	#end if
+	$summarize
+	#for $input in $inputs
+		${input.input}
+	#end for
+</command>
+
+<inputs>
+	<repeat name="inputs" title="BLAST result">
+		<param name="input" format="tabular" type="data" label="BLAST result"/>
+	</repeat>
+	<param name="factor" type="float" value="10" label="E-value factor" help="For each query, hits with e-values within this factor of the best hit's e-value will be included when computing the lowest common ancestor (or picking randomly)."/>
+	<param name="random" type="boolean" truevalue="-r" falsevalue="" label="Random" help="Pick from hits within E-value factor randomly instead of finding the lowest common ancestor"/>
+	<param name="score" type="select" label="Score by">
+		<option value="evalue">E-value</option>
+		<option value="percentIdentity">Percent identity</option>
+		<option value="bitScore">Bit score</option>
+	</param>
+	<param name="summarize" type="boolean" truevalue="-s" falsevalue="" label="Summarize" help="Sum results by taxonomy ID and list totals in the first column instead of query IDs"/>
+</inputs>
+
+<outputs>
+	<data format="tabular" name="output"/>
+</outputs>
+
+<help>
+
+**What it does**
+
+Creates taxonomic classifications for each query in BLAST results by finding the lowest common ancestor (or by picking randomly, if specified) of "best" hits (as determined by e-value factor above). Requires a KronaTools_ installation (2.0 or higher) with taxonomy downloaded.
+
+ .. _KronaTools: http://krona.sourceforge.net
+
+**Input**
+
+Tabular BLAST results containing gi numbers. If comment lines are present, queries with no hits will be assigned to taxon -1 (consistent with MEGAN).
+
+Example input (BLAST)::
+
+  1      2                            3      4    5  6  7  8    9        10       11     12
+  read1  gi|211853080|gb|EQ846228.1|  97.33  150  1  3  6  154  9518999  9519146  5e-64  252
+  read2  gi|211853080|gb|EQ846228.1|  96.69  151  0  5  6  154  9496147  9496294  2e-62  246
+
+**Output**
+
+The output is a list of query IDs (or counts, if **summarize** is specified) followed by NCBI taxonomy IDs and scores. This can be used to create a Krona chart by specifying "Taxonomy ID list" as the **input type**. If the output is summarized, the **summarized** option must also be specified when creating the chart.
+
+Example output (default)::
+
+  1 (query ID)  2 (tax ID)  3 (score)
+  read1         9606        94.34
+  read2         9616        32.17
+
+Example output (summarized)::
+
+  1 (count)  2 (tax ID)  3 (score)
+  243        9606        94.34
+  17         9616        32.17
+
+</help>
+  <requirements>
+  	<requirement type="binary">ktClassifyBLAST</requirement>
+  </requirements>
+</tool>
diff -r f8fdde273a2a -r 53258f6dddd3 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Oct 29 13:52:47 2012 -0500
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="KronaTools" version="2.2">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/krona/files/KronaTools%20%28Mac%2C%20Linux%29/KronaTools-2.2.tar</action>
+                <!-- Instaead of $INSTALL_DIR/  this could be in a data dir -->
+                <action type="make_directory">$INSTALL_DIR/taxonomy</action>
+                <action type="shell_command">perl install.pl --prefix $INSTALL_DIR --taxonomy $INSTALL_DIR/taxonomy</action>
+                <action type="shell_command">./updateTaxonomy.sh</action>
+                <!-- copy javascript to galaxy/static/krona/ dir 
+                <action type="shell_command">./deployResources.sh /static/krona</action>
+                -->
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>http://sourceforge.net/p/krona/home/krona/</readme>
+    </package>
+</tool_dependency>