# HG changeset patch
# User iuc
# Date 1662052499 0
# Node ID 06c5b883632d3c60313b73c10aa8e62395a2ed30

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1

diff -r 000000000000 -r 06c5b883632d dram_set_database_locations.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dram_set_database_locations.py	Thu Sep 01 17:14:59 2022 +0000
@@ -0,0 +1,102 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+import subprocess
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('--db_version', action='store', dest='db_version', help='Version of DRAM databases')
+parser.add_argument('--skip_uniref', action='store_true', dest='skip_uniref', default=False, help='Flag to Download and process uniref')
+parser.add_argument('--galaxy_data_manager_data_path', action='store', dest='galaxy_data_manager_data_path', help='Absolute Galaxy data manager data path')
+parser.add_argument('--output', action='store', dest='output', help='Output file')
+
+args = parser.parse_args()
+
+
+def get_new_dram_config_entry(db_version, old_entry, new_base_path):
+    # Example old_entry:
+    # KOfam db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/kofam_profiles.hmm
+    base_path, file_name = os.path.split(old_entry)
+    # The new entry must be GALAXY_DATA_MANAGER_DATA_PATH/DRAM/${value}/file_name
+    return os.path.join(new_base_path, 'DRAM', db_version, file_name)
+
+
+# At this point the DRAM config will look something like this.
+# Processed search databases
+# KEGG db: None
+# KOfam db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/kofam_profiles.hmm
+# KOfam KO list: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/kofam_ko_list.tsv
+# UniRef db: None
+# Pfam db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/pfam.mmspro
+# dbCAN db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/dbCAN-HMMdb-V10.txt
+# RefSeq Viral db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/refseq_viral.20220707.mmsdb
+# MEROPS peptidase db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/peptidases.20220707.mmsdb
+# VOGDB db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/vog_latest_hmms.txt
+#
+# Descriptions of search database entries
+# Pfam hmm dat: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/Pfam-A.hmm.dat.gz
+# dbCAN family activities: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/CAZyDB.07292021.fam-activities.txt
+# VOG annotations: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/vog_annotations_latest.tsv.gz
+#
+# Description db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/description_db.sqlite
+#
+# DRAM distillation sheets
+# Genome summary form: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/genome_summary_form.20220707.tsv
+# Module step form: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/module_step_form.20220707.tsv
+# ETC module database: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/etc_mdoule_database.20220707.tsv
+# Function heatmap form: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/function_heatmap_form.20220707.tsv
+# AMG database: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/amg_database.20220707.tsv
+
+# Write the current DRAM CONFIG to a file for processing.
+cmd = 'DRAM-setup.py print_config > dram_config.txt'
+subprocess.check_call(cmd, shell=True)
+
+# Update the database locations that DRAM sets in it's CONFIG
+# to point to the configured GALAXY_DATA_MANAGER_DATA_PATH location
+# for the DRAM databases.
+cmd = 'DRAM-setup.py set_database_locations'
+with open('dram_config.txt', 'r') as fh:
+    for line in fh:
+        line = line.rstrip('\r\n')
+        if line.startswith('KOfam db:'):
+            cmd = '%s --kofam_hmm_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('KOfam KO list:'):
+            cmd = '%s --kofam_ko_list_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('UniRef db:'):
+            if not args.skip_uniref:
+                cmd = '%s --uniref_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('Pfam db:'):
+            cmd = '%s --pfam_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('dbCAN db:'):
+            cmd = '%s --dbcan_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('RefSeq Viral db:'):
+            cmd = '%s --viral_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('MEROPS peptidase db:'):
+            cmd = '%s --peptidase_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('VOGDB db:'):
+            cmd = '%s --vogdb_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('Pfam hmm dat:'):
+            cmd = '%s --pfam_hmm_dat %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('dbCAN family activities:'):
+            cmd = '%s --dbcan_fam_activities %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('VOG annotations:'):
+            cmd = '%s --vog_annotations %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('Description db:'):
+            cmd = '%s --description_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('Genome summary form:'):
+            cmd = '%s --genome_summary_form_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('Module step form:'):
+            cmd = '%s --module_step_form_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('ETC module database:'):
+            cmd = '%s --etc_module_database_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('Function heatmap form:'):
+            cmd = '%s --function_heatmap_form_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+        elif line.startswith('AMG database:'):
+            cmd = '%s --amg_database_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
+cmd = '%s --update_description_db' % cmd
+subprocess.check_call(cmd, shell=True)
+
+# Write the new DRAM CONFIG to a file to the output.
+cmd = 'DRAM-setup.py print_config > %s' % args.output
+subprocess.check_call(cmd, shell=True)
diff -r 000000000000 -r 06c5b883632d dram_set_database_locations.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dram_set_database_locations.xml	Thu Sep 01 17:14:59 2022 +0000
@@ -0,0 +1,52 @@
+<tool id="dram_set_database_locations" name="DRAM: set database locations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>after installation by the data manager</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/dram_set_database_locations.py'
+$skip_uniref
+--db_version '$db_version'
+--galaxy_data_manager_data_path '$galaxy_data_manager_data_path'
+--output '$output'
+    ]]></command>
+    <inputs>
+        <param argument="--skip_uniref" type="boolean" truevalue="--skip_uniref" falsevalue="" checked="false" label="Did you skip downloading and processing uniref when you installed the DRAM databases?"/>
+        <param name="db_version" type="text" value="1.3.5" label="DRAM database version">
+            <expand macro="sanitizer"/>
+        </param>
+        <param name="galaxy_data_manager_data_path" type="text" value="" label="Absolute Galaxy data manager data path" help="This is the absolute path for the Galaxy tool-data config setting">
+            <expand macro="sanitizer"/>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt"/>
+    </outputs>
+    <tests>
+        <test expect_failure="true">
+            <param name="skip_uniref" value="true"/>
+            <param name="galaxy_data_manager_data_path" value="/gx/tool-data"/>
+            <assert_stderr>
+                <has_text text="error: unrecognized arguments: db: None"/>
+            </assert_stderr>
+        </test>
+    </tests>
+    <help>
+Use of this tool should be restricted to a Galaxy administrator.  This tool updates the DRAM configuration file
+with the location of the databases after installation by the data manager.  This is necessary because DRAM creates
+a configuration file during installation, but the file is written before the Galaxy job finishes, so the database
+locations are relative to the job working directory instead of the configured GALAXY_DATA_MANAGER_DATA_PATH.
+
+It may be more ideal to perform this task as a second step in the data manager tool, but DRAM will not allow
+the configuration file to be updated to point to locations unless the databases exist in those locations.  But
+the data manager tool moves the databases to these locations as its last step, making it impossible to update
+the DRAM configuration file as a second step of that tool.
+
+See https://github.com/WrightonLabCSU/DRAM/wiki/5.-Managing%2C-updating-or-moving-a-DRAM-installation-and-databases for details.
+    </help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkaa621</citation>
+    </citations>
+</tool>
+
diff -r 000000000000 -r 06c5b883632d macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Sep 01 17:14:59 2022 +0000
@@ -0,0 +1,23 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.3.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">20.09</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">dram</requirement>
+        </requirements>
+    </xml>
+    <xml name="sanitizer">
+        <sanitizer invalid_char="">
+            <valid initial="string.printable">
+                <remove value="&apos;"/>
+            </valid>
+        </sanitizer>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/s13104-016-1900-2</citation>
+        </citations>
+    </xml>
+</macros>
+