Mercurial > repos > iuc > data_manager_dram_database_downloader
comparison 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 |
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date | Thu, 01 Sep 2022 17:16:07 +0000 |
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1 <tool id="data_manager_dram_download" name="DRAM: Download databases" version="1.3.5" tool_type="manage_data" profile="21.05"> | |
2 <description>required by the DRAM suite of tools</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.3.5">dram</requirement> | |
5 </requirements> | |
6 <command detect_errors="exit_code"><![CDATA[ | |
7 python '$__tool_directory__/data_manager_dram_download.py' | |
8 --out_file '$out_file' | |
9 #if str($kofam_hmm_loc) != '': | |
10 --kofam_hmm_loc '$kofam_hmm_loc' | |
11 #end if | |
12 #if str($kofam_ko_list_loc) != '': | |
13 --kofam_ko_list_loc '$kofam_ko_list_loc' | |
14 #end if | |
15 #if str($skip_uniref_cond.skip_uniref) == 'yes': | |
16 --skip_uniref '$skip_uniref_cond.skip_uniref' | |
17 #else: | |
18 #if str($skip_uniref_cond.uniref_loc) != '': | |
19 --uniref_loc '$skip_uniref_cond.uniref_loc' | |
20 #end if | |
21 --uniref_version $skip_uniref_cond.uniref_version | |
22 #end if | |
23 #if str($pfam_loc) != '': | |
24 --pfam_loc '$pfam_loc' | |
25 #end if | |
26 #if str($pfam_hmm_dat) != '': | |
27 --pfam_hmm_dat '$pfam_hmm_dat' | |
28 #end if | |
29 #if str($dbcan_loc) != '': | |
30 --dbcan_loc '$dbcan_loc' | |
31 #end if | |
32 #if str($dbcan_fam_activities) != '': | |
33 --dbcan_fam_activities '$dbcan_fam_activities' | |
34 #end if | |
35 --dbcan_version $dbcan_version | |
36 #if str($vogdb_loc) != '': | |
37 --vogdb_loc '$vogdb_loc' | |
38 #end if | |
39 #if str($vog_annotations) != '': | |
40 --vog_annotations '$vog_annotations' | |
41 #end if | |
42 #if str($viral_loc) != '': | |
43 --viral_loc '$viral_loc' | |
44 #end if | |
45 #if str($peptidase_loc) != '': | |
46 --peptidase_loc '$peptidase_loc' | |
47 #end if | |
48 #if str($genome_summary_form_loc) != '': | |
49 --genome_summary_form_loc '$genome_summary_form_loc' | |
50 #end if | |
51 #if str($module_step_form_loc) != '': | |
52 --module_step_form_loc '$module_step_form_loc' | |
53 #end if | |
54 #if str($etc_module_database_loc) != '': | |
55 --etc_module_database_loc '$etc_module_database_loc' | |
56 #end if | |
57 #if str($function_heatmap_form_loc) != '': | |
58 --function_heatmap_form_loc '$function_heatmap_form_loc' | |
59 #end if | |
60 #if str($amg_database_loc) != '': | |
61 --amg_database_loc '$amg_database_loc' | |
62 #end if | |
63 --threads \${GALAXY_SLOTS:-10} | |
64 --db_version '$db_version' | |
65 ]]></command> | |
66 <inputs> | |
67 <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"> | |
68 <sanitizer invalid_char=""> | |
69 <valid initial="string.printable"> | |
70 <remove value="'"/> | |
71 </valid> | |
72 </sanitizer> | |
73 </param> | |
74 <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"> | |
75 <sanitizer invalid_char=""> | |
76 <valid initial="string.printable"> | |
77 <remove value="'"/> | |
78 </valid> | |
79 </sanitizer> | |
80 </param> | |
81 | |
82 <conditional name="skip_uniref_cond"> | |
83 <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"> | |
84 <option value="no" selected="true">No</option> | |
85 <option value="yes">Yes</option> | |
86 </param> | |
87 <when value="no"> | |
88 <param argument="--uniref_loc" type="text" value="" label="Absolute path to uniref (uniref90.fasta.gz) if already installed" help="Leave blank to install"> | |
89 <sanitizer invalid_char=""> | |
90 <valid initial="string.printable"> | |
91 <remove value="'"/> | |
92 </valid> | |
93 </sanitizer> | |
94 </param> | |
95 <param argument="--uniref_version" type="integer" value="90" label="UniRef version to download" help="Ignored if uniref is not downloaded and processed"/> | |
96 </when> | |
97 <when value="yes"/> | |
98 </conditional> | |
99 <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"> | |
100 <sanitizer invalid_char=""> | |
101 <valid initial="string.printable"> | |
102 <remove value="'"/> | |
103 </valid> | |
104 </sanitizer> | |
105 </param> | |
106 <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"> | |
107 <sanitizer invalid_char=""> | |
108 <valid initial="string.printable"> | |
109 <remove value="'"/> | |
110 </valid> | |
111 </sanitizer> | |
112 </param> | |
113 <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"> | |
114 <sanitizer invalid_char=""> | |
115 <valid initial="string.printable"> | |
116 <remove value="'"/> | |
117 </valid> | |
118 </sanitizer> | |
119 </param> | |
120 <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"> | |
121 <sanitizer invalid_char=""> | |
122 <valid initial="string.printable"> | |
123 <remove value="'"/> | |
124 </valid> | |
125 </sanitizer> | |
126 </param> | |
127 <param argument="--dbcan_version" type="integer" value="10" label="Version of dbCAN to use"/> | |
128 <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"> | |
129 <sanitizer invalid_char=""> | |
130 <valid initial="string.printable"> | |
131 <remove value="'"/> | |
132 </valid> | |
133 </sanitizer> | |
134 </param> | |
135 <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"> | |
136 <sanitizer invalid_char=""> | |
137 <valid initial="string.printable"> | |
138 <remove value="'"/> | |
139 </valid> | |
140 </sanitizer> | |
141 </param> | |
142 <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"> | |
143 <sanitizer invalid_char=""> | |
144 <valid initial="string.printable"> | |
145 <remove value="'"/> | |
146 </valid> | |
147 </sanitizer> | |
148 </param> | |
149 <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"> | |
150 <sanitizer invalid_char=""> | |
151 <valid initial="string.printable"> | |
152 <remove value="'"/> | |
153 </valid> | |
154 </sanitizer> | |
155 </param> | |
156 <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"> | |
157 <sanitizer invalid_char=""> | |
158 <valid initial="string.printable"> | |
159 <remove value="'"/> | |
160 </valid> | |
161 </sanitizer> | |
162 </param> | |
163 <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"> | |
164 <sanitizer invalid_char=""> | |
165 <valid initial="string.printable"> | |
166 <remove value="'"/> | |
167 </valid> | |
168 </sanitizer> | |
169 </param> | |
170 <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"> | |
171 <sanitizer invalid_char=""> | |
172 <valid initial="string.printable"> | |
173 <remove value="'"/> | |
174 </valid> | |
175 </sanitizer> | |
176 </param> | |
177 <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"> | |
178 <sanitizer invalid_char=""> | |
179 <valid initial="string.printable"> | |
180 <remove value="'"/> | |
181 </valid> | |
182 </sanitizer> | |
183 </param> | |
184 <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"> | |
185 <sanitizer invalid_char=""> | |
186 <valid initial="string.printable"> | |
187 <remove value="'"/> | |
188 </valid> | |
189 </sanitizer> | |
190 </param> | |
191 <param argument="--db_version" type="text" value="1.3.5" label="Version of DRAM databases to install"> | |
192 <sanitizer invalid_char=""> | |
193 <valid initial="string.printable"> | |
194 <remove value="'"/> | |
195 </valid> | |
196 </sanitizer> | |
197 </param> | |
198 </inputs> | |
199 <outputs> | |
200 <data name="out_file" format="data_manager_json"/> | |
201 </outputs> | |
202 <tests> | |
203 <test expect_failure="true"> | |
204 <param name="kofam_hmm_loc" value="profiles.tar.gz"/> | |
205 <param name="kofam_ko_list_loc" value="ko_list.gz"/> | |
206 <param name="skip_uniref" value="yes"/> | |
207 <param name="pfam_loc" value="Pfam-A.full.gz"/> | |
208 <param name="pfam_hmm_dat" value="Pfam-A.hmm.dat.gz"/> | |
209 <param name="dbcan_loc" value="dbCAN-HMMdb-V9.txt"/> | |
210 <param name="dbcan_fam_activities" value="CAZyDB.07302020.fam-activities.txt"/> | |
211 <param name="vogdb_loc" value="vog.hmm.tar.gz"/> | |
212 <param name="vog_annotations" value="vog.annotations.tsv.gz"/> | |
213 <param name="viral_loc" value="viral.x.protein.faa.gz"/> | |
214 <param name="peptidase_loc" value="pepunit.lib"/> | |
215 <param name="genome_summary_form_loc" value="genome_summary_form.20220715.tsv"/> | |
216 <param name="module_step_form_loc" value="module_step_form.20220715.tsv"/> | |
217 <param name="etc_module_database_loc" value="etc_mdoule_database.20220715.tsv"/> | |
218 <param name="function_heatmap_form_loc" value="function_heatmap_form.20220715.tsv"/> | |
219 <param name="amg_database_loc" value="amg_database.20220715.tsv"/> | |
220 <assert_stderr> | |
221 <has_text text="Database location does not exist"/> | |
222 </assert_stderr> | |
223 </test> | |
224 </tests> | |
225 <help> | |
226 This tool downloads and processes DRAM databases for annotation and makes them available to corresponding versions | |
227 of the DRAM suite of tools. | |
228 | |
229 See https://github.com/WrightonLabCSU/DRAM/wiki for details about DRAM. | |
230 </help> | |
231 <citations> | |
232 <citation type="doi">10.1093/nar/gkaa621</citation> | |
233 </citations> | |
234 </tool> | |
235 |