Mercurial > repos > galaxyp > dbbuilder
changeset 6:3425a176dff2 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit b1ccd85b9c91cf311f92e6b9999fddd6d2408b20"
| author | galaxyp |
|---|---|
| date | Sun, 13 Sep 2020 08:33:43 +0000 |
| parents | cc23650fc85e |
| children | 8e263cd38da1 |
| files | dbbuilder.xml |
| diffstat | 1 files changed, 2 insertions(+), 36 deletions(-) [+] |
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--- a/dbbuilder.xml Wed May 03 09:53:02 2017 -0400 +++ b/dbbuilder.xml Sun Sep 13 08:33:43 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