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comparison data_manager/data_manager_dram_download.xml @ 0:bd342a6a5b0f draft

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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
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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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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="&apos;"/>
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