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dbbuilder.xml uniprot_taxons.loc.sample |
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| diff -r 6c624803c5f9 -r a38cd98a6b41 dbbuilder.xml --- a/dbbuilder.xml Fri May 10 17:09:36 2013 -0400 +++ b/dbbuilder.xml Fri Jul 12 12:57:50 2013 -0400 |
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| @@ -29,20 +29,20 @@ </command> <inputs> <conditional name="source"> - <param name="from" type="select" label="Download from"> + <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"> <option value="uniprot">UniProtKB</option> <option value="cRAP">cRAP (contaminants)</option> <option value="url">Custom URL</option> </param> <when value="uniprot"> - <param name="taxon" type="select" format="text" > + <param name="taxon" type="select" format="text" help="select species for protein database"> <label>Taxonomy</label> <options from_file="uniprot_taxons.loc"> <column name="name" index="0" /> <column name="value" index="1" /> </options> </param> - <param name="reviewed" type="select"> + <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%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option> <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option> @@ -62,7 +62,7 @@ </valid> </sanitizer> </param> - <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" /> + <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="url"> @@ -82,8 +82,14 @@ <help> **Output** -A FASTA file containing the specified protein sequences. +Creates a FASTA file of specified protein sequences for comparison with experimental MS/MS data in search algorithm. + +**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 +.. _UniProtKB: http://www.uniprot.org/help/uniprotkb </help> </tool> |
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| diff -r 6c624803c5f9 -r a38cd98a6b41 uniprot_taxons.loc.sample --- a/uniprot_taxons.loc.sample Fri May 10 17:09:36 2013 -0400 +++ b/uniprot_taxons.loc.sample Fri Jul 12 12:57:50 2013 -0400 |
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| @@ -7,4 +7,8 @@ Arabidopsis thaliana (Mouse-ear cress) 3702 Caenorhabditis elegans (C.elegans) 6239 Drosophila melanogaster (Fruit fly) 7227 -Saccharomyces cerevisiae (Baker's Yeast) 4932 \ No newline at end of file +Saccharomyces cerevisiae (Baker's Yeast) 4932 +Canis familiaris (Dog) 9615 +Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 64091 +Apis mellifera (Honeybee) 7460 +Mycobacterium tuberculosis H37Rv (MTB) [Not complete proteome] 83332 |