Mercurial > repos > galaxyp > dbbuilder
changeset 9:0f641df3f28a 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 21:57:06 +0000 |
| parents | 3f6354b7eb94 |
| children | |
| files | dbbuilder.xml |
| diffstat | 1 files changed, 54 insertions(+), 17 deletions(-) [+] |
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--- a/dbbuilder.xml Tue Sep 27 13:21:28 2022 +0000 +++ b/dbbuilder.xml Tue Sep 27 21:57:06 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="dbbuilder" name="Protein Database Downloader" version="0.3.3"> +<tool id="dbbuilder" name="Protein Database Downloader" version="0.3.4"> <description></description> <requirements> <requirement type="package" version="1.20.1">wget</requirement> @@ -16,17 +16,20 @@ <command> <![CDATA[ #if $source.from == "uniprot" - #if $source.set: - #set $modified_set = '&' + str($source.set) - #else - #set $modified_set = '' - #end if + #set $query_fields = [] #if $source.taxon_id - #set $taxon_id = $source.taxon_id + #silent $query_fields.append('taxonomy_id:' + str($source.taxon_id)) #else - #set $taxon_id = $source.taxon + #silent $query_fields.append('taxonomy_id:' + str($source.taxon)) + #end if + #if $source.reviewed: + #silent $query_fields.append(str($source.reviewed)) #end if - #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) + #if $source.set: + #silent $query_fields.append(str($source.set)) + #end if + #set $query = '(' + ')+AND+('.join($query_fields) + ')' + #set $url = 'https://rest.uniprot.org/uniprotkb/stream?compressed=true&format=fasta' + str($source.include_isoform) + '&query=' + $query #set $type = "uniprotkb_stream" #elif $source.from == "cRAP" ##set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" @@ -85,24 +88,24 @@ <param name="taxon_id" type="integer" value="" min="1" optional="true" help="Specify a NCBI taxon id to override species selection"/> <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"> <option value="">UniProtKB</option> - <option value="+reviewed%3Atrue">UniProtKB/Swiss-Prot (reviewed only)</option> - <option value="+reviewed%3Afalse">UniProtKB/TrEMBL (unreviewed only)</option> + <option value="reviewed:true">UniProtKB/Swiss-Prot (reviewed only)</option> + <option value="reviewed:false">UniProtKB/TrEMBL (unreviewed only)</option> <sanitizer> <valid> - <add value="%"/> + <add value=":"/> </valid> </sanitizer> </param> <param name="set" type="select" label="Proteome Set"> <option value="">Any</option> - <option value="keyword%3aKW-1185" selected="true">Reference Proteome Set</option> + <option value="keyword:KW-1185" selected="true">Reference Proteome Set</option> <sanitizer> <valid> - <add value="%"/> + <add value=":"/> </valid> </sanitizer> </param> - <param name="include_isoform" type="boolean" truevalue="&includeIsoform=true" falsevalue="" + <param name="include_isoform" type="boolean" truevalue="&includeIsoform=true" falsevalue="" label="Include isoform data" help="several different forms of a given protein are incorporated into database" /> </when> <when value="cRAP" /> @@ -168,11 +171,12 @@ </assert_contents> </output> </test> + <test> <conditional name="source"> <param name="from" value="uniprot" /> <param name="taxon_id" value="2697049"/> - <param name="reviewed" value="+reviewed%3Atrue"/> + <param name="reviewed" value="reviewed:true"/> <param name="set" value=""/> </conditional> <output name="output_database"> @@ -182,11 +186,12 @@ </assert_contents> </output> </test> + <test> <conditional name="source"> <param name="from" value="uniprot" /> <param name="taxon_id" value="2697049"/> - <param name="reviewed" value="+reviewed%3Afalse"/> + <param name="reviewed" value="reviewed:false"/> <param name="set" value=""/> </conditional> <output name="output_database"> @@ -198,6 +203,38 @@ </test> <test> + <conditional name="source"> + <param name="from" value="uniprot" /> + <param name="taxon" value="83333"/> + <param name="reviewed" value="reviewed:true"/> + <param name="set" value=""/> + <param name="include_isoform" value="True"/> + </conditional> + <output name="output_database"> + <assert_contents> + <has_text text="sp|P06615|REDF_ECOLI" /> + <has_text text=">sp|P06710-2|DPO3X_ECOLI" /> + </assert_contents> + </output> + </test> + <test> + <conditional name="source"> + <param name="from" value="uniprot" /> + <param name="taxon" value="83333"/> + <param name="reviewed" value="reviewed:true"/> + <param name="set" value=""/> + <param name="include_isoform" value="False"/> + </conditional> + <output name="output_database"> + <assert_contents> + <has_text text="sp|P06615|REDF_ECOLI" /> + <has_text text="REDF_ECOLI" /> + <not_has_text text=">sp|P06710-2|DPO3X_ECOLI" /> + </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" />