Mercurial > repos > iuc > data_manager_dram_database_downloader
diff data_manager/data_manager_dram_download.xml @ 0:bd342a6a5b0f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
author | iuc |
---|---|
date | Thu, 01 Sep 2022 17:16:07 +0000 |
parents | |
children |
line wrap: on
line diff
--- /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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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="'"/> + </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> +