Mercurial > repos > galaxyp > dbbuilder
changeset 8:a85fbebe8b2f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit baa8095b41984515948c6ef2fda7c7e61c945f94
| author | galaxyp |
|---|---|
| date | Wed, 03 May 2017 09:53:17 -0400 |
| parents | a94dc3d469cb |
| children | c1b437242fee |
| files | dbbuilder.xml |
| diffstat | 1 files changed, 123 insertions(+), 9 deletions(-) [+] |
line wrap: on
line diff
--- a/dbbuilder.xml Tue May 02 08:52:01 2017 -0400 +++ b/dbbuilder.xml Wed May 03 09:53:17 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="dbbuilder" name="Protein Database Downloader" version="0.2.1"> +<tool id="dbbuilder" name="Protein Database Downloader" version="0.3.0"> <description></description> <requirements> <requirement type="package">gnu-wget</requirement> @@ -20,20 +20,46 @@ ##set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" #set $url = "https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta" #set $type = "direct" + #elif $source.from == "HMP" + #set $url = 'http://downloads.hmpdacc.org/data/reference_genomes/body_sites/' + str($source.site) + '.pep.fsa' + #set $type = "direct" + #elif $source.from == "HOMD" + #set $url = 'ftp://ftp.homd.org/human_oral_microbial_genomic_sequences/current/' + str($source.annotation) + #if str($source.annotation).endswith('.tar.gz'): + #set $type = "tgz" + #elif str($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 = "direct" + #set $type = $source.archive_type #end if #if $type =="direct" - wget -nv '$url' -O '${output_database}' + wget -nv '$url' -O '${output_database}' --no-check-certificate + #elif $type =="zip" + wget -nv '$url' -O tmp.zip --no-check-certificate && zcat -c tmp.zip > '${output_database}' + #elif $type =="gzip" + wget -nv '$url' -O tmp.gz --no-check-certificate && (if `command -v gzcat > /dev/null`; then gzcat tmp.gz; else zcat tmp.gz ; fi) > '${output_database}' + #elif $type =="bzip2" + wget -nv '$url' -O tmp.bz2 --no-check-certificate && bzcat tmp.bz2 > '${output_database}' + #elif $type =="tgz" + wget -nv '$url' -O tmp.tar.gz && tar zxfO tmp.tar.gz > '${output_database}' + #elif $type =="tbz" + wget -nv '$url' -O tmp.tar.bz && tar jxfO tmp.tar.bz > '${output_database}' #end if ]]> </command> <inputs> <conditional name="source"> - <param name="from" type="select" label="Download from" help="Select database source. cRAP acts as a database for common MS contaminants. UniProtKB is a corss species collection of functional protein databases"> + <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"> <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> <when value="uniprot"> @@ -67,19 +93,60 @@ <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" help="several different forms of a given protein are incorporated into database" /> </when> <when value="cRAP" /> + <when value="HMP"> + <param name="site" type="select" label="Proteome for body site"> + <option value="Airways">HMP airways</option> + <option value="Blood">HMP Blood</option> + <option value="Gastrointestinal_tract">HMP Gastro-intestinal tract</option> + <option value="Oral">HMP Oral</option> + <option value="Skin">HMP Skin</option> + <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> + <option value="oral_microbiome.aa.tar.gz">HOMD with static annotation</option> + </param> + </when> <when value="url"> - <param name="url" value="" type="text" label="URL (http, ftp)"> + <param name="url" value="" type="text" label="URL (http, ftp) of Fasta sequences"> <sanitizer> <valid> <add value="%"/> + <add value="~"/> </valid> </sanitizer> </param> + <param name="archive_type" type="select" label="Fasta source compression type"> + <option value="direct" selected="true">fasta file (uncompressed)</option> + <option value="gzip">fasta.gz (gzip compressed)</option> + <option value="bzip2">fasta.bz2 (bzip2 compressed)</option> + <option value="zip">fasta.zip or fasta.Z (Zip compressed)</option> + <option value="tgz">fasta.tgz or fasta.tar.gz (tar archive gzip compressed)</option> + <option value="tbz">fasta.tbz or fasta.tar.bz (tar archive bzip2 compressed)</option> + </param> </when> </conditional> </inputs> <outputs> - <data format="fasta" name="output_database" label="Protein Database" /> + <data format="fasta" name="output_database" label="Protein Database ${source.from}" /> </outputs> <tests> <test> @@ -90,6 +157,28 @@ </assert_contents> </output> </test> + <test> + <param name="from" value="url" /> + <param name="url" value="https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta" /> + <param name="archive_type" value="direct" /> + <output name="output_database"> + <assert_contents> + <has_text text="KKA1_ECOLX" /> + </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[ @@ -99,11 +188,36 @@ **External Links** -_Galaxy-P 101 shows usage Protein Database Downloader tool in the creation of a workflow -.. _Galaxy-P 101: http://msi-galaxy-p.readthedocs.org/en/latest/sections/galaxyp_101.html -_UniProtKB provides additional information about the UniProt Knowledgebase + - Galaxy-P_101_ shows usage Protein Database Downloader tool in the creation of a workflow + - UniProtKB_ provides additional information about the UniProt Knowledgebase + + +.. _Galaxy-P_101: http://msi-galaxy-p.readthedocs.org/en/latest/sections/galaxyp_101.html .. _UniProtKB: http://www.uniprot.org/help/uniprotkb + + +**Additional Protein Fasta URLs** + + *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 + + ]]> </help> + <citations> + <citation type="doi">10.1093/nar/gkw1099</citation> + <citation type="doi">10.1093/nar/gkv1195 </citation> + <citation type="doi">10.1093/database/baq013</citation> + <citation type="doi">10.1038/nature11209</citation> + <citation type="doi">10.1038/nature11234</citation> + </citations> </tool>