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comparison dbbuilder.xml @ 9:c1b437242fee draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit b1ccd85b9c91cf311f92e6b9999fddd6d2408b20"
author galaxyp
date Sun, 13 Sep 2020 08:34:00 +0000
parents a85fbebe8b2f
children e9df53a75f3c
comparison
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8:a85fbebe8b2f 9:c1b437242fee
1 <tool id="dbbuilder" name="Protein Database Downloader" version="0.3.0"> 1 <tool id="dbbuilder" name="Protein Database Downloader" version="0.3.1">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package">gnu-wget</requirement> 4 <requirement type="package" version="1.20.1">wget</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" level="fatal" description="Error downloading database." /> 7 <exit_code range="1:" level="fatal" description="Error downloading database." />
8 <regex match="ERROR" level="fatal" source="stderr" description="Error downloading database." /> 8 <regex match="ERROR" level="fatal" source="stderr" description="Error downloading database." />
9 </stdio> 9 </stdio>
28 #if str($source.annotation).endswith('.tar.gz'): 28 #if str($source.annotation).endswith('.tar.gz'):
29 #set $type = "tgz" 29 #set $type = "tgz"
30 #elif str($source.annotation).endswith('.zip'): 30 #elif str($source.annotation).endswith('.zip'):
31 #set $type = "zip" 31 #set $type = "zip"
32 #end if 32 #end if
33 #elif $source.from == 'EBI Metagenomics'
34 #set $url = 'https://www.ebi.ac.uk/metagenomics/projects/' + str($source.ebi_project) + '/samples/' + str($source.ebi_sample) + '/runs/' + str($source.ebi_run) + '/results/versions/' + str($source.ebi_version) + '/sequences/' + str($source.ebi_annotation) + '/chunks/1'
35 #set $type = "gzip"
36 #elif $source.from == "url" 33 #elif $source.from == "url"
37 #set $url = $source.url 34 #set $url = $source.url
38 #set $type = $source.archive_type 35 #set $type = $source.archive_type
39 #end if 36 #end if
40 #if $type =="direct" 37 #if $type =="direct"
56 <conditional name="source"> 53 <conditional name="source">
57 <param name="from" type="select" label="Download from" help="Select database source. cRAP acts as a database for common MS contaminants. UniProtKB is a cross species collection of functional protein databases"> 54 <param name="from" type="select" label="Download from" help="Select database source. cRAP acts as a database for common MS contaminants. UniProtKB is a cross species collection of functional protein databases">
58 <option value="uniprot">UniProtKB</option> 55 <option value="uniprot">UniProtKB</option>
59 <option value="cRAP">cRAP (contaminants)</option> 56 <option value="cRAP">cRAP (contaminants)</option>
60 <option value="HMP">Human Microbiome Project body sites</option> 57 <option value="HMP">Human Microbiome Project body sites</option>
61 <option value="EBI Metagenomics">EBI Metagenomics</option>
62 <option value="HOMD">Human Oral Microbiome Database (HOMD)</option> 58 <option value="HOMD">Human Oral Microbiome Database (HOMD)</option>
63 <option value="url">Custom URL</option> 59 <option value="url">Custom URL</option>
64 </param> 60 </param>
65 <when value="uniprot"> 61 <when value="uniprot">
66 <param name="taxon" type="select" format="text" help="select species for protein database"> 62 <param name="taxon" type="select" format="text" help="select species for protein database">
100 <option value="Gastrointestinal_tract">HMP Gastro-intestinal tract</option> 96 <option value="Gastrointestinal_tract">HMP Gastro-intestinal tract</option>
101 <option value="Oral">HMP Oral</option> 97 <option value="Oral">HMP Oral</option>
102 <option value="Skin">HMP Skin</option> 98 <option value="Skin">HMP Skin</option>
103 <option value="Urogenital_tract">HMP urogenital Tract</option> 99 <option value="Urogenital_tract">HMP urogenital Tract</option>
104 </param> 100 </param>
105 </when>
106 <when value="EBI Metagenomics">
107 <param name="ebi_project" value="" type="text" label="EBI Metagenomics Project (e.g. DRP003095)">
108 <help><![CDATA[
109 Look up EBI Metagenomics at https://www.ebi.ac.uk/metagenomics/search
110 ]]></help>
111 </param>
112 <param name="ebi_sample" value="" type="text" label="EBI Metagenomics Sample (e.g. DRS029200)">
113 </param>
114 <param name="ebi_run" value="" type="text" label="EBI Metagenomics Run (e.g. DRR033743)">
115 </param>
116 <param name="ebi_version" value="" type="text" label="EBI Metagenomics Pipeline Version (e.g. 3.0)">
117 </param>
118 <param name="ebi_annotation" type="boolean" label="With Annotation" checked="true"
119 truevalue="PredictedCDSWithAnnotation" falsevalue="PredictedCDSWithioutAnnotation"/>
120
121 </when> 101 </when>
122 <when value="HOMD"> 102 <when value="HOMD">
123 <param name="annotation" type="select" label="Human Oral Microbiome Proteome"> 103 <param name="annotation" type="select" label="Human Oral Microbiome Proteome">
124 <option value="oral_microbiome_dynamic.aa.zip">HOMD with dynamic annotation</option> 104 <option value="oral_microbiome_dynamic.aa.zip">HOMD with dynamic annotation</option>
125 <option value="oral_microbiome.aa.tar.gz">HOMD with static annotation</option> 105 <option value="oral_microbiome.aa.tar.gz">HOMD with static annotation</option>
165 <assert_contents> 145 <assert_contents>
166 <has_text text="KKA1_ECOLX" /> 146 <has_text text="KKA1_ECOLX" />
167 </assert_contents> 147 </assert_contents>
168 </output> 148 </output>
169 </test> 149 </test>
170 <test>
171 <param name="from" value="EBI Metagenomics" />
172 <param name="ebi_project" value="DRP003095" />
173 <param name="ebi_sample" value="DRS029200" />
174 <param name="ebi_run" value="DRR033743" />
175 <param name="ebi_version" value="3.0" />
176 <output name="output_database">
177 <assert_contents>
178 <has_text text="DRR033743" />
179 </assert_contents>
180 </output>
181 </test>
182 </tests> 150 </tests>
183 <help> 151 <help>
184 <![CDATA[ 152 <![CDATA[
185 **Output** 153 **Output**
186 154
198 166
199 **Additional Protein Fasta URLs** 167 **Additional Protein Fasta URLs**
200 168
201 *HUMAN GUT METAPROTEOME:* 169 *HUMAN GUT METAPROTEOME:*
202 170
203 * 512MB gzip ftp://public.genomics.org.cn/BGI/gutmeta/UniSet/UniGene.pep.gz
204 * 61MB gzip http://www.bork.embl.de/~arumugam/Qin_et_al_2010/frequent_microbe_proteins.fasta.gz 171 * 61MB gzip http://www.bork.embl.de/~arumugam/Qin_et_al_2010/frequent_microbe_proteins.fasta.gz
205 172
206 173
207 *MOUSE GUT MICROBIOTA:* 174 *MOUSE GUT MICROBIOTA:*
208 175
209 * 417MB gzip ftp://climb.genomics.cn/pub/10.5524/100001_101000/100114/Genecatalog/184sample_2.6M.GeneSet.pep.gz
210 * See: http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP 176 * See: http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP
211 177
212 178
213 ]]> 179 ]]>
214 </help> 180 </help>