comparison dbbuilder.xml @ 3:a38cd98a6b41 draft

Uploaded

2:6c624803c5f9

    wget -nv '$url' -O '${output_database}'
    #end if
  </command>
  <inputs>
    <conditional name="source">
      <param name="from" type="select" label="Download from">
        <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" >
          <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">
          <option value="+">UniProtKB</option>
          <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option>
          <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option>
          <sanitizer>
            <valid>

            <valid>
              <add value="%"/>
            </valid>
          </sanitizer>
        </param>
        <param name="include_isoform" type="boolean" truevalue="&amp;include=yes" falsevalue="" label="Include isoform data" />
      </when>
      <when value="cRAP" />
      <when value="url">
        <param name="url" value="" type="text" label="URL (http, ftp)">
          <sanitizer>

    <data format="fasta" name="output_database" label="Protein Database" />
  </outputs>
  <help>
**Output**

A FASTA file containing the specified protein sequences.

  </help>
</tool>

3:a38cd98a6b41

    wget -nv '$url' -O '${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">
        <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" 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" 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>
          <sanitizer>
            <valid>

            <valid>
              <add value="%"/>
            </valid>
          </sanitizer>
        </param>
        <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">
        <param name="url" value="" type="text" label="URL (http, ftp)">
          <sanitizer>

    <data format="fasta" name="output_database" label="Protein Database" />
  </outputs>
  <help>
**Output**

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>