# HG changeset patch
# User p.lucas
# Date 1673510354 0
# Node ID 2d0679d0d8f7549911120e324d780c3fc7a7eb9f
# Parent  a0cb48398130ba2414727131209f38bcdc2a200a
Uploaded classify blast

diff -r a0cb48398130 -r 2d0679d0d8f7 classify_blast.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/classify_blast.xml	Thu Jan 12 07:59:14 2023 +0000
@@ -0,0 +1,80 @@
+<tool id="classify_blast" name="Classify BLAST" version="1.0.0">
+<description>results using KronaTools</description>
+
+<requirements>
+  <requirement name="package" version="2.8.1">krona</requirement>
+</requirements>
+
+<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>