# HG changeset patch
# User galaxyp
# Date 1373648270 14400
# Node ID a38cd98a6b411a44f089a6b5b9441b8f1c2d10f1
# Parent  6c624803c5f93c2f806ad2304912bf55f01fb30b
Uploaded

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
@@ -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="&amp;include=yes" falsevalue="" label="Include isoform data" />
+        <param name="include_isoform" type="boolean" truevalue="&amp;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>
 
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
@@ -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