Mercurial > repos > galaxyp > dbbuilder
comparison dbbuilder.xml @ 12:983bf725dfc2 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit b3726245d52acb0d0efcb46ef978d75e2b0f2453
author | galaxyp |
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date | Tue, 27 Sep 2022 21:57:37 +0000 |
parents | 8e637098a8ab |
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11:8e637098a8ab | 12:983bf725dfc2 |
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1 <tool id="dbbuilder" name="Protein Database Downloader" version="0.3.3"> | 1 <tool id="dbbuilder" name="Protein Database Downloader" version="0.3.4"> |
2 <description></description> | 2 <description></description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.20.1">wget</requirement> | 4 <requirement type="package" version="1.20.1">wget</requirement> |
5 <requirement type="package" version="3.8">python</requirement> | 5 <requirement type="package" version="3.8">python</requirement> |
6 <requirement type="package" version="2.20.1">requests</requirement> | 6 <requirement type="package" version="2.20.1">requests</requirement> |
14 <!-- http://maxquant.org/contaminants.zip --> | 14 <!-- http://maxquant.org/contaminants.zip --> |
15 <!-- ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz--> | 15 <!-- ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz--> |
16 <command> | 16 <command> |
17 <![CDATA[ | 17 <![CDATA[ |
18 #if $source.from == "uniprot" | 18 #if $source.from == "uniprot" |
19 #set $query_fields = [] | |
20 #if $source.taxon_id | |
21 #silent $query_fields.append('taxonomy_id:' + str($source.taxon_id)) | |
22 #else | |
23 #silent $query_fields.append('taxonomy_id:' + str($source.taxon)) | |
24 #end if | |
25 #if $source.reviewed: | |
26 #silent $query_fields.append(str($source.reviewed)) | |
27 #end if | |
19 #if $source.set: | 28 #if $source.set: |
20 #set $modified_set = '&' + str($source.set) | 29 #silent $query_fields.append(str($source.set)) |
21 #else | |
22 #set $modified_set = '' | |
23 #end if | 30 #end if |
24 #if $source.taxon_id | 31 #set $query = '(' + ')+AND+('.join($query_fields) + ')' |
25 #set $taxon_id = $source.taxon_id | 32 #set $url = 'https://rest.uniprot.org/uniprotkb/stream?compressed=true&format=fasta' + str($source.include_isoform) + '&query=' + $query |
26 #else | |
27 #set $taxon_id = $source.taxon | |
28 #end if | |
29 #set $url = 'https://rest.uniprot.org/uniprotkb/stream?compressed=true&format=fasta&query=taxonomy_id:"' + str($taxon_id) + '"' + str($modified_set) + str($source.reviewed) + str($source.include_isoform) | |
30 #set $type = "uniprotkb_stream" | 33 #set $type = "uniprotkb_stream" |
31 #elif $source.from == "cRAP" | 34 #elif $source.from == "cRAP" |
32 ##set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" | 35 ##set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" |
33 #set $url = "https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta" | 36 #set $url = "https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta" |
34 #set $type = "direct" | 37 #set $type = "direct" |
83 </options> | 86 </options> |
84 </param> | 87 </param> |
85 <param name="taxon_id" type="integer" value="" min="1" optional="true" help="Specify a NCBI taxon id to override species selection"/> | 88 <param name="taxon_id" type="integer" value="" min="1" optional="true" help="Specify a NCBI taxon id to override species selection"/> |
86 <param name="reviewed" type="select" help="UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database- may contain redundant sequences, but there is a higher chance peptides will be identified. UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database- less of a chance peptides will be identified but less sequence redundancy"> | 89 <param name="reviewed" type="select" help="UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database- may contain redundant sequences, but there is a higher chance peptides will be identified. UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database- less of a chance peptides will be identified but less sequence redundancy"> |
87 <option value="">UniProtKB</option> | 90 <option value="">UniProtKB</option> |
88 <option value="+reviewed%3Atrue">UniProtKB/Swiss-Prot (reviewed only)</option> | 91 <option value="reviewed:true">UniProtKB/Swiss-Prot (reviewed only)</option> |
89 <option value="+reviewed%3Afalse">UniProtKB/TrEMBL (unreviewed only)</option> | 92 <option value="reviewed:false">UniProtKB/TrEMBL (unreviewed only)</option> |
90 <sanitizer> | 93 <sanitizer> |
91 <valid> | 94 <valid> |
92 <add value="%"/> | 95 <add value=":"/> |
93 </valid> | 96 </valid> |
94 </sanitizer> | 97 </sanitizer> |
95 </param> | 98 </param> |
96 <param name="set" type="select" label="Proteome Set"> | 99 <param name="set" type="select" label="Proteome Set"> |
97 <option value="">Any</option> | 100 <option value="">Any</option> |
98 <option value="keyword%3aKW-1185" selected="true">Reference Proteome Set</option> | 101 <option value="keyword:KW-1185" selected="true">Reference Proteome Set</option> |
99 <sanitizer> | 102 <sanitizer> |
100 <valid> | 103 <valid> |
101 <add value="%"/> | 104 <add value=":"/> |
102 </valid> | 105 </valid> |
103 </sanitizer> | 106 </sanitizer> |
104 </param> | 107 </param> |
105 <param name="include_isoform" type="boolean" truevalue="&includeIsoform=true" falsevalue="" | 108 <param name="include_isoform" type="boolean" truevalue="&includeIsoform=true" falsevalue="" |
106 label="Include isoform data" help="several different forms of a given protein are incorporated into database" /> | 109 label="Include isoform data" help="several different forms of a given protein are incorporated into database" /> |
107 </when> | 110 </when> |
108 <when value="cRAP" /> | 111 <when value="cRAP" /> |
109 <when value="HMP"> | 112 <when value="HMP"> |
110 <param name="site" type="select" label="Proteome for body site"> | 113 <param name="site" type="select" label="Proteome for body site"> |
166 <assert_contents> | 169 <assert_contents> |
167 <has_text text="SPIKE_SARS2" /> | 170 <has_text text="SPIKE_SARS2" /> |
168 </assert_contents> | 171 </assert_contents> |
169 </output> | 172 </output> |
170 </test> | 173 </test> |
174 | |
171 <test> | 175 <test> |
172 <conditional name="source"> | 176 <conditional name="source"> |
173 <param name="from" value="uniprot" /> | 177 <param name="from" value="uniprot" /> |
174 <param name="taxon_id" value="2697049"/> | 178 <param name="taxon_id" value="2697049"/> |
175 <param name="reviewed" value="+reviewed%3Atrue"/> | 179 <param name="reviewed" value="reviewed:true"/> |
176 <param name="set" value=""/> | 180 <param name="set" value=""/> |
177 </conditional> | 181 </conditional> |
178 <output name="output_database"> | 182 <output name="output_database"> |
179 <assert_contents> | 183 <assert_contents> |
180 <has_text text=">sp|P0DTC1|R1A_SARS2" /> | 184 <has_text text=">sp|P0DTC1|R1A_SARS2" /> |
181 <not_has_text text=">tr|A0A679G4D8|A0A679G4D8_SARS2" /> | 185 <not_has_text text=">tr|A0A679G4D8|A0A679G4D8_SARS2" /> |
182 </assert_contents> | 186 </assert_contents> |
183 </output> | 187 </output> |
184 </test> | 188 </test> |
189 | |
185 <test> | 190 <test> |
186 <conditional name="source"> | 191 <conditional name="source"> |
187 <param name="from" value="uniprot" /> | 192 <param name="from" value="uniprot" /> |
188 <param name="taxon_id" value="2697049"/> | 193 <param name="taxon_id" value="2697049"/> |
189 <param name="reviewed" value="+reviewed%3Afalse"/> | 194 <param name="reviewed" value="reviewed:false"/> |
190 <param name="set" value=""/> | 195 <param name="set" value=""/> |
191 </conditional> | 196 </conditional> |
192 <output name="output_database"> | 197 <output name="output_database"> |
193 <assert_contents> | 198 <assert_contents> |
194 <has_text text=">tr|A0A679G4D8|A0A679G4D8_SARS2" /> | 199 <has_text text=">tr|A0A679G4D8|A0A679G4D8_SARS2" /> |
195 <not_has_text text=">sp|P0DTC1|R1A_SARS2" /> | 200 <not_has_text text=">sp|P0DTC1|R1A_SARS2" /> |
201 </assert_contents> | |
202 </output> | |
203 </test> | |
204 | |
205 <test> | |
206 <conditional name="source"> | |
207 <param name="from" value="uniprot" /> | |
208 <param name="taxon" value="83333"/> | |
209 <param name="reviewed" value="reviewed:true"/> | |
210 <param name="set" value=""/> | |
211 <param name="include_isoform" value="True"/> | |
212 </conditional> | |
213 <output name="output_database"> | |
214 <assert_contents> | |
215 <has_text text="sp|P06615|REDF_ECOLI" /> | |
216 <has_text text=">sp|P06710-2|DPO3X_ECOLI" /> | |
217 </assert_contents> | |
218 </output> | |
219 </test> | |
220 <test> | |
221 <conditional name="source"> | |
222 <param name="from" value="uniprot" /> | |
223 <param name="taxon" value="83333"/> | |
224 <param name="reviewed" value="reviewed:true"/> | |
225 <param name="set" value=""/> | |
226 <param name="include_isoform" value="False"/> | |
227 </conditional> | |
228 <output name="output_database"> | |
229 <assert_contents> | |
230 <has_text text="sp|P06615|REDF_ECOLI" /> | |
231 <has_text text="REDF_ECOLI" /> | |
232 <not_has_text text=">sp|P06710-2|DPO3X_ECOLI" /> | |
196 </assert_contents> | 233 </assert_contents> |
197 </output> | 234 </output> |
198 </test> | 235 </test> |
199 | 236 |
200 <test> | 237 <test> |