# HG changeset patch
# User galaxyp
# Date 1599986040 0
# Node ID c1b437242fee7283b46835a9f236f8286f72af7e
# Parent  a85fbebe8b2ff8fbf8aef4b8165ad0f93c1b8a0e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit b1ccd85b9c91cf311f92e6b9999fddd6d2408b20"

diff -r a85fbebe8b2f -r c1b437242fee dbbuilder.xml
--- a/dbbuilder.xml	Wed May 03 09:53:17 2017 -0400
+++ b/dbbuilder.xml	Sun Sep 13 08:34:00 2020 +0000
@@ -1,7 +1,7 @@
-<tool id="dbbuilder" name="Protein Database Downloader" version="0.3.0">
+<tool id="dbbuilder" name="Protein Database Downloader" version="0.3.1">
     <description></description>
     <requirements>
-        <requirement type="package">gnu-wget</requirement>
+        <requirement type="package" version="1.20.1">wget</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:"  level="fatal" description="Error downloading database." />
@@ -30,9 +30,6 @@
             #elif str($source.annotation).endswith('.zip'):
                 #set $type = "zip" 
             #end if 
-        #elif $source.from == 'EBI Metagenomics'
-            #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'
-            #set $type = "gzip"
         #elif $source.from == "url"
             #set $url = $source.url
             #set $type = $source.archive_type
@@ -58,7 +55,6 @@
                 <option value="uniprot">UniProtKB</option>
                 <option value="cRAP">cRAP (contaminants)</option>
                 <option value="HMP">Human Microbiome Project body sites</option>
-                <option value="EBI Metagenomics">EBI Metagenomics</option>
                 <option value="HOMD">Human Oral Microbiome Database (HOMD)</option>
                 <option value="url">Custom URL</option>
             </param>
@@ -103,22 +99,6 @@
                     <option value="Urogenital_tract">HMP urogenital Tract</option>
                 </param>
             </when>
-            <when value="EBI Metagenomics">
-                <param name="ebi_project" value="" type="text" label="EBI Metagenomics Project (e.g. DRP003095)">
-                <help><![CDATA[
-Look up EBI Metagenomics at https://www.ebi.ac.uk/metagenomics/search 
-                ]]></help>
-                </param>
-                <param name="ebi_sample" value="" type="text" label="EBI Metagenomics Sample (e.g. DRS029200)">
-                </param>
-                <param name="ebi_run" value="" type="text" label="EBI Metagenomics Run (e.g. DRR033743)">
-                </param>
-                <param name="ebi_version" value="" type="text" label="EBI Metagenomics Pipeline Version (e.g. 3.0)">
-                </param>
-                <param name="ebi_annotation" type="boolean" label="With Annotation" checked="true" 
-                      truevalue="PredictedCDSWithAnnotation" falsevalue="PredictedCDSWithioutAnnotation"/>
-                      
-            </when>
             <when value="HOMD">
                 <param name="annotation" type="select" label="Human Oral Microbiome Proteome">
                     <option value="oral_microbiome_dynamic.aa.zip">HOMD with dynamic annotation</option>
@@ -167,18 +147,6 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
-            <param name="from" value="EBI Metagenomics" />
-            <param name="ebi_project" value="DRP003095" />
-            <param name="ebi_sample" value="DRS029200" />
-            <param name="ebi_run" value="DRR033743" />
-            <param name="ebi_version" value="3.0" />
-            <output name="output_database">
-                <assert_contents>
-                    <has_text text="DRR033743" />
-                </assert_contents>
-            </output>
-        </test>
     </tests>
     <help>
 <![CDATA[
@@ -200,13 +168,11 @@
 
   *HUMAN GUT METAPROTEOME:*
 
-    * 512MB gzip ftp://public.genomics.org.cn/BGI/gutmeta/UniSet/UniGene.pep.gz
     *  61MB gzip http://www.bork.embl.de/~arumugam/Qin_et_al_2010/frequent_microbe_proteins.fasta.gz
 
 
   *MOUSE GUT MICROBIOTA:*
 
-    * 417MB gzip ftp://climb.genomics.cn/pub/10.5524/100001_101000/100114/Genecatalog/184sample_2.6M.GeneSet.pep.gz
     * See: http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP