diff kraken-report.xml @ 0:f2757ab26483 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kraken-report.xml	Thu Jul 23 10:56:14 2015 -0400
@@ -0,0 +1,49 @@
+<tool id="kraken-report" name="Kraken-report" version="1.1.0">
+    <description>
+        view a sample report of your classification
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+        <![CDATA[
+        @SET_DATABASE_PATH@ &&
+        kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report"
+        ]]>
+    </command>
+    <inputs>
+        <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/>
+        <expand macro="input_database" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output_report" />
+    </outputs>
+    <help>
+<![CDATA[
+
+.. class:: warningmark
+
+**Note**: the database used must be the same as the one used in the original Kraken run
+
+-----
+
+**Output**
+
+The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows::
+
+ 1. Percentage of reads covered by the clade rooted at this taxon
+ 2. Number of reads covered by the clade rooted at this taxon
+ 3. Number of reads assigned directly to this taxon
+ 4. A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply filled with a dash.
+ 5. NCBI taxonomy ID
+ 6. Indented scientific name
+
+The scientific names are indented using spaces, according to the tree
+structure specified by the taxonomy.
+    ]]>
+    </help>
+    <expand macro="version_command" />
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="citations" />
+</tool>