Mercurial > repos > dfornika > data_manager_build_kraken2_database

changeset 1:f9a7275b1cad draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9b4d704c147761201fa9f1450fcf5ba6871104d8-dirty
author dfornika
date Wed, 27 Feb 2019 20:48:06 -0500
parents b1805f086b66
children 18523fd8bec9
files data_manager/kraken2_custom_database_builder.xml data_manager/kraken2_database_builder.xml data_manager/kraken2_standard_database_builder.xml data_manager_conf.xml
diffstat 4 files changed, 67 insertions(+), 52 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_custom_database_builder.xml	Wed Feb 27 20:48:06 2019 -0500
@@ -0,0 +1,50 @@
+<?xml version="1.0"?>
+<tool id="kraken2_custom_database_builder" name="Kraken2 Custom Database Builder" tool_type="manage_data" version="2.0.7_beta">
+    <description>database builder</description>
+    <requirements>
+        <requirement type="package" version="2.0.7_beta">kraken2</requirement>
+    </requirements>
+    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
+    <command detect_errors="exit_code">
+    <![CDATA[
+        #set $library_list = str($libraries).split(',')
+        mkdir kraken2-database && cd kraken2-database &&
+        kraken2-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' &&
+        #for $library in $library_list:
+            #if str($library) != 'None':
+                kraken2-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' &&
+            #end if
+        #end for
+        #for $fasta in $input_fasta:
+            #if str($fasta) != 'None':
+                kraken2-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' &&
+            #end if
+        #end for
+        kraken2-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} &&
+        cd .. &&
+        python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}'
+    ]]>
+    </command>
+    <inputs>
+        <param name="database_name" type="text" label="Name for this database" />
+        <param name="libraries" type="select" multiple="true" label="Select partial library to download">
+            <option value="archaea">Archaea</option>
+	    <option value="bacteria">Bacteria</option>
+            <option value="plasmid">Plasmid</option>
+            <option value="viral">Viral</option>
+            <option value="human">Human</option>
+        </param>
+        <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" />
+        <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
+        <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
+	<param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <help>
+    </help>
+    <citations>
+        <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
+    </citations>
+</tool>
--- a/data_manager/kraken2_database_builder.xml	Wed Feb 27 20:42:33 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-<?xml version="1.0"?>
-<tool id="kraken2_database_builder" name="Kraken" tool_type="manage_data" version="2.0.7_beta">
-    <description>database builder</description>
-    <requirements>
-        <requirement type="package" version="2.0.7_beta">kraken2</requirement>
-    </requirements>
-    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
-    <command detect_errors="exit_code">
-    <![CDATA[
-        #set $library_list = str($libraries).split(',')
-        mkdir kraken2-database && cd kraken2-database &&
-        kraken2-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' &&
-        #for $library in $library_list:
-            #if str($library) != 'None':
-                kraken2-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' &&
-            #end if
-        #end for
-        #for $fasta in $input_fasta:
-            #if str($fasta) != 'None':
-                kraken2-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' &&
-            #end if
-        #end for
-        kraken2-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} &&
-        cd .. &&
-        python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}'
-    ]]>
-    </command>
-    <inputs>
-        <param name="database_name" type="text" label="Name for this database" />
-        <param name="libraries" type="select" multiple="true" label="Select partial library to download">
-            <option value="archaea">Archaea</option>
-	    <option value="bacteria">Bacteria</option>
-            <option value="plasmid">Plasmid</option>
-            <option value="viral">Viral</option>
-            <option value="human">Human</option>
-        </param>
-        <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" />
-        <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
-        <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
-	<param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
-    </inputs>
-    <outputs>
-        <data name="out_file" format="data_manager_json" />
-    </outputs>
-    <help>
-    </help>
-    <citations>
-        <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
-    </citations>
-</tool>
--- a/data_manager/kraken2_standard_database_builder.xml	Wed Feb 27 20:42:33 2019 -0500
+++ b/data_manager/kraken2_standard_database_builder.xml	Wed Feb 27 20:48:06 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="kraken2_standard_database_builder" name="Kraken" tool_type="manage_data" version="2.0.7_beta">
+<tool id="kraken2_standard_database_builder" name="Kraken2 Standard Database Builder" tool_type="manage_data" version="2.0.7_beta">
     <description>database builder</description>
     <requirements>
         <requirement type="package" version="2.0.7_beta">kraken2</requirement>
--- a/data_manager_conf.xml	Wed Feb 27 20:42:33 2019 -0500
+++ b/data_manager_conf.xml	Wed Feb 27 20:48:06 2019 -0500
@@ -1,5 +1,20 @@
 <data_managers>
-    <data_manager tool_file="data_manager/kraken2_database_builder.xml" id="kraken2_database_builder" version="1.0">
+    <data_manager tool_file="data_manager/kraken2_custom_database_builder.xml" id="kraken2_custom_database_builder" version="1.0">
+	<data_table name="kraken2_databases">
+	    <output>
+		<column name="value"/>
+		<column name="name"/>
+		<column name="path" output_ref="out_file">
+		    <move type="directory" relativize_symlinks="True">
+			<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_database/${value}</target>
+		    </move>
+		    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_database/${value}</value_translation>
+		    <value_translation type="function">abspath</value_translation>
+		</column>
+	    </output>
+	</data_table>
+    </data_manager>
+    <data_manager tool_file="data_manager/kraken2_standard_database_builder.xml" id="kraken2_standard_database_builder" version="1.0">
 	<data_table name="kraken2_databases">
 	    <output>
 		<column name="value"/>