diff data_manager/kraken_database_builder.xml @ 0:d5d803e654dd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken_database_builder.xml	Wed Apr 22 09:11:37 2015 -0400
@@ -0,0 +1,46 @@
+<?xml version="1.0"?>
+<tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.0.0">
+    <description>database builder</description>
+    <requirements>
+        <requirement type="package" version="0.10.5">kraken</requirement>
+        <requirement type="package" version="1.1.11">jellyfish</requirement>
+        <requirement type="set_environment">KRAKEN_SCRIPT_PATH</requirement>
+    </requirements>
+    <stdio>
+        <exit_code description="Error" level="fatal" range="1:" />
+    </stdio>
+    <version_command>kraken -version | awk '{print $NF}'</version_command>
+    <command>
+    <![CDATA[
+        #set $library_list = str($libraries).split(',')
+        mkdir kraken-database && cd kraken-database &&
+        kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db "${database_name}" &&
+        #for $library in $library_list:
+            kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db "${database_name}"  &&
+        #end for
+        #for $fasta in $input_fasta:
+            kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta"  &&
+        #end for
+        kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len}  &&
+        cd .. && python \$KRAKEN_SCRIPT_PATH/data_manager/make_json.py --db "${database_name}" --out "${out_file}"
+    ]]>
+    </command>
+    <inputs>
+        <param label="Name for this database" name="database_name" type="text" />
+        <param label="Select partial library to download" multiple="True" name="libraries" type="select">
+            <option value="bacteria">Bacteria</option>
+            <option value="plasmids">Plasmids</option>
+            <option value="viruses">Viruses</option>
+            <option value="human">Human</option>
+        </param>
+        <param format="fasta" label="Select history item" multiple="True" name="input_fasta" type="data" />
+        <param label="K-mer length in BP" name="kmer_len" type="integer" value="31" />
+        <param label="Minimizer length" name="minimizer_len" type="integer" value="15" />
+    </inputs>
+    <outputs>
+        <data format="data_manager_json" name="out_file" />
+    </outputs>
+    <citations>
+        <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
+    </citations>
+</tool>
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