changeset 0:9cf44596402a draft

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bracken commit 0b1a602e21fbf8cfeba1294b6b985f1fba75afe9-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/est-abundance.xml	Mon Apr 01 06:52:24 2019 -0400
@@ -0,0 +1,51 @@
+<tool id="bracken" name="Bracken" version="@VERSION@">
+    <description>Bayesian Reestimation of Abundance with KrakEN</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+    est_abundance.py \
+    -i $input \
+    -k $kmer_distr \
+    -l $level \
+    -t $threshold \
+    -o $report
+    ]]>
+    </command>
+    
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Kraken report file" />
+        <!-- DATABASE INPUT-->
+        <param label="Select a Kmer distribution" name="kmer_distr" type="select">
+            <options from_data_table="bracken_databases">
+                <validator message="No database is available" type="no_options" />
+            </options>
+        </param>
+        <param name="level" type="select" label="Level" help="Level to push all reads to" >
+            <option value="S" selected="true">Species</option>
+            <option value="G">Genus</option>
+            <option value="F">Family</option>
+            <option value="O">Order</option>
+            <option value="C">Class</option>
+            <option value="P">Phylum</option>
+            <option value="D">Domain</option>
+        </param>
+        <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag" help="Threshold for the minimum number of reads kraken must
+                        assign to a classification for that classification to
+                        be considered in the final abundance estimation." />
+        
+    </inputs>
+
+    <outputs>
+        <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
+    </outputs>
+
+    <expand macro="citations" />    
+    <help>
+    <![CDATA[
+
+        Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_.
+    ]]></help>
+
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Apr 01 06:52:24 2019 -0400
@@ -0,0 +1,14 @@
+<macros>
+    <token name="@VERSION@">2.2</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">bracken</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.7717/peerj-cs.104</citation>
+        </citations>
+    </xml>
+</macros>
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bracken_databases.loc.sample	Mon Apr 01 06:52:24 2019 -0400
@@ -0,0 +1,3 @@
+# This file defines databases and their folder location. Each database is a line with 
+# three columns: value{tab}{name}{/path/to/database-file} 
+# E.g. database100mers{tab}database100mers{tab}/home/user/bracken_databases/database100mers.kmer_distrib

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Apr 01 06:52:24 2019 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of ariba database in the required format -->
+    <table name="bracken_databases" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, path</columns>
+        <file path="tool-data/bracken_databases.loc" />
+    </table>
+</tables>
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