diff kraken-filter.xml @ 0:cbb802a726fd draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kraken-filter.xml	Thu Jul 23 10:56:00 2015 -0400
@@ -0,0 +1,54 @@
+<tool id="kraken-filter" name="Kraken-filter" version="1.1.0">
+    <description>
+        filter classification by confidence score
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+        <![CDATA[
+        @SET_DATABASE_PATH@ &&
+        kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output"
+        ]]>
+    </command>
+    <inputs>
+        <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/>
+        <param label="Confidence threshold" max="1" min="0" name="threshold" type="float" value="0" help="--threshold; A number between 0 and 1; default=0"/>
+        <expand macro="input_database" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="filtered_output" />
+    </outputs>
+    <help>
+<![CDATA[
+
+.. class:: warningmark
+
+**Note**: the database used must be the same as the one used in the original Kraken run
+
+-----
+
+**What it does**
+
+At present, we have not yet developed a confidence score with a solid probabilistic interpretation for Kraken. However, we have developed a simple scoring scheme that has yielded good results for us, and we've made that available in the kraken-filter script. The approach we use allows a user to specify a threshold score in the [0,1] interval; the ``kraken-filter`` script then will adjust labels up the tree until the label's score (described below) meets or exceeds that threshold. If a label at the root of the taxonomic tree would not have a score exceeding the threshold, the sequence is called unclassified by ``kraken-filter``.
+
+A sequence label's score is a fraction C/Q, where C is the number of k-mers mapped to LCA values in the clade rooted at the label, and Q is the number of k-mers in the sequence that lack an ambiguous nucleotide (i.e., they were queried against the database). Consider the example of the LCA mappings in Kraken's output::
+
+ 562:13 561:4 A:31 0:1 562:3 
+
+would indicate that::
+
+ the first 13 k-mers mapped to taxonomy ID #562
+ the next 4 k-mers mapped to taxonomy ID #561
+ the next 31 k-mers contained an ambiguous nucleotide
+ the next k-mer was not in the database
+ the last 3 k-mers mapped to taxonomy ID #562
+
+In this case, ID #561 is the parent node of #562. Here, a label of #562 for this sequence would have a score of C/Q = (13+3)/(13+4+1+3) = 16/21. A label of #561 would have a score of C/Q = (13+4+3)/(13+4+1+3) = 20/21. If a user specified a threshold over 16/21, kraken-filter would adjust the original label from #562 to #561; if the threshold was greater than 20/21, the sequence would become unclassified.
+    ]]>
+    </help>
+    <expand macro="version_command" />
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="citations" />
+</tool>