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
date Tue, 27 Sep 2022 21:57:37 +0000
parents 8e637098a8ab
children
comparison
equal deleted inserted replaced
11:8e637098a8ab 12:983bf725dfc2
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="&amp;includeIsoform=true" falsevalue="" 108 <param name="include_isoform" type="boolean" truevalue="&amp;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>