--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_dram_download.xml	Thu Sep 01 17:16:07 2022 +0000
@@ -0,0 +1,235 @@
+<tool id="data_manager_dram_download" name="DRAM: Download databases" version="1.3.5" tool_type="manage_data" profile="21.05">
+    <description>required by the DRAM suite of tools</description>
+    <requirements>
+        <requirement type="package" version="1.3.5">dram</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/data_manager_dram_download.py'
+--out_file '$out_file'
+#if str($kofam_hmm_loc) != '':
+    --kofam_hmm_loc '$kofam_hmm_loc'
+#end if
+#if str($kofam_ko_list_loc) != '':
+    --kofam_ko_list_loc '$kofam_ko_list_loc'
+#end if
+#if str($skip_uniref_cond.skip_uniref) == 'yes':
+    --skip_uniref '$skip_uniref_cond.skip_uniref'
+#else:
+    #if str($skip_uniref_cond.uniref_loc) != '':
+        --uniref_loc '$skip_uniref_cond.uniref_loc'
+    #end if
+    --uniref_version $skip_uniref_cond.uniref_version
+#end if
+#if str($pfam_loc) != '':
+    --pfam_loc '$pfam_loc'
+#end if
+#if str($pfam_hmm_dat) != '':
+    --pfam_hmm_dat '$pfam_hmm_dat'
+#end if
+#if str($dbcan_loc) != '':
+    --dbcan_loc '$dbcan_loc'
+#end if
+#if str($dbcan_fam_activities) != '':
+    --dbcan_fam_activities '$dbcan_fam_activities'
+#end if
+--dbcan_version $dbcan_version
+#if str($vogdb_loc) != '':
+    --vogdb_loc '$vogdb_loc'
+#end if
+#if str($vog_annotations) != '':
+    --vog_annotations '$vog_annotations'
+#end if
+#if str($viral_loc) != '':
+    --viral_loc '$viral_loc'
+#end if
+#if str($peptidase_loc) != '':
+    --peptidase_loc '$peptidase_loc'
+#end if
+#if str($genome_summary_form_loc) != '':
+    --genome_summary_form_loc '$genome_summary_form_loc'
+#end if
+#if str($module_step_form_loc) != '':
+    --module_step_form_loc '$module_step_form_loc'
+#end if
+#if str($etc_module_database_loc) != '':
+    --etc_module_database_loc '$etc_module_database_loc'
+#end if
+#if str($function_heatmap_form_loc) != '':
+    --function_heatmap_form_loc '$function_heatmap_form_loc'
+#end if
+#if str($amg_database_loc) != '':
+    --amg_database_loc '$amg_database_loc'
+#end if
+--threads \${GALAXY_SLOTS:-10}
+--db_version '$db_version'
+    ]]></command>
+    <inputs>
+        <param argument="--kofam_hmm_loc" type="text" value="" label="Absolute path to hmm file for KOfam (profiles.tar.gz) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--kofam_ko_list_loc" type="text" value="" label="Absolute path to KOfam ko list file (ko_list.gz) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+
+        <conditional name="skip_uniref_cond">
+            <param argument="--skip_uniref" type="select" label="Skip downloading and processing uniref?" help="Choosing Yes saves time and memory and does not impact DRAM distillation">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+                <param argument="--uniref_loc" type="text" value="" label="Absolute path to uniref (uniref90.fasta.gz) if already installed" help="Leave blank to install">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.printable">
+                            <remove value="&apos;"/>
+                        </valid>
+                    </sanitizer>
+                </param>
+                <param argument="--uniref_version" type="integer" value="90" label="UniRef version to download" help="Ignored if uniref is not downloaded and processed"/>
+            </when>
+            <when value="yes"/>
+        </conditional>
+        <param argument="--pfam_loc" type="text" value="" label="Absolute path to pfam-A full file (Pfam-A.full.gz) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--pfam_hmm_dat" type="text" value="" label="Absolute path to pfam hmm .dat file to get PF descriptions (Pfam-A.hmm.dat.gz) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--dbcan_loc" type="text" value="" label="Absolute path to dbCAN file (dbCAN-HMMdb-V9.txt) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--dbcan_fam_activities" type="text" value="" label="Absolute path to CAZY family activities file (CAZyDB.07302020.fam-activities.txt) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--dbcan_version" type="integer" value="10" label="Version of dbCAN to use"/>
+        <param argument="--vogdb_loc" type="text" value="" label="Absolute path to hmm file for vogdb (vog.hmm.tar.gz) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--vog_annotations" type="text" value="" label="Absolute path to vogdb annotations file (vog.annotations.tsv.gz) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--viral_loc" type="text" value="" label="Absolute path to merged viral protein faa file (viral.x.protein.faa.gz) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--peptidase_loc" type="text" value="" label="Absolute path to MEROPS peptidase fasta file (pepunit.lib) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--genome_summary_form_loc" type="text" value="" label="Absolute path to genome summary form file (genome_summary_form.YYYYMMDD.tsv) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--module_step_form_loc" type="text" value="" label="Absolute path to module step form file (module_step_form.YYYYMMDD.tsv) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--etc_module_database_loc" type="text" value="" label="Absolute path to etc module database file (etc_mdoule_database.YYYYMMDD.tsv) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--function_heatmap_form_loc" type="text" value="" label="Absolute path to function heatmap form file (function_heatmap_form.YYYYMMDD.tsv) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--amg_database_loc" type="text" value="" label="Absolute path to amg database file (amg_database.YYYYMMDD.tsv) if already installed" help="Leave blank to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--db_version" type="text" value="1.3.5" label="Version of DRAM databases to install">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <test expect_failure="true">
+            <param name="kofam_hmm_loc" value="profiles.tar.gz"/>
+            <param name="kofam_ko_list_loc" value="ko_list.gz"/>
+            <param name="skip_uniref" value="yes"/>
+            <param name="pfam_loc" value="Pfam-A.full.gz"/>
+            <param name="pfam_hmm_dat" value="Pfam-A.hmm.dat.gz"/>
+            <param name="dbcan_loc" value="dbCAN-HMMdb-V9.txt"/>
+            <param name="dbcan_fam_activities" value="CAZyDB.07302020.fam-activities.txt"/>
+            <param name="vogdb_loc" value="vog.hmm.tar.gz"/>
+            <param name="vog_annotations" value="vog.annotations.tsv.gz"/>
+            <param name="viral_loc" value="viral.x.protein.faa.gz"/>
+            <param name="peptidase_loc" value="pepunit.lib"/>
+            <param name="genome_summary_form_loc" value="genome_summary_form.20220715.tsv"/>
+            <param name="module_step_form_loc" value="module_step_form.20220715.tsv"/>
+            <param name="etc_module_database_loc" value="etc_mdoule_database.20220715.tsv"/>
+            <param name="function_heatmap_form_loc" value="function_heatmap_form.20220715.tsv"/>
+            <param name="amg_database_loc" value="amg_database.20220715.tsv"/>
+            <assert_stderr>
+                <has_text text="Database location does not exist"/>
+            </assert_stderr>
+        </test>
+    </tests>
+    <help>
+This tool downloads and processes DRAM databases for annotation and makes them available to corresponding versions
+of the DRAM suite of tools.
+
+See https://github.com/WrightonLabCSU/DRAM/wiki for details about DRAM.
+    </help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkaa621</citation>
+    </citations>
+</tool>
+