<tool id="scaffold" name="Scaffold" version="0.1.0">
  <description>
    Visualize and Validate Complex MS/MS Proteomics Experiments
  </description>
  <configfiles>
    <configfile name="sample_config"># Simple format group:group_name followed by pairs of name:name and path:path lines
#if $sample_mode.mode == "full"
#set $samples = $sample_mode.samples
#for $sample in $samples:
#if $sample.category.specify
#set $category = $sample.category.name
#else
#set $category = $sample.sample_name
#end if
sample:$sample.sample_name
mudpit:$sample.mudpit
category:$category
#for $sample_input in $sample.sample_inputs:
name:${sample_input.display_name}
path:${sample_input}
ext:${sample_input.ext}
#end for
#end for
#elif $sample_mode.mode == "sample_per_file":
#for $sample_input in $sample_mode.sample_inputs:
sample:${sample_input.display_name}
mudpit:false
category:${sample_input.display_name}
name:${sample_input.display_name}
path:${sample_input}
ext:${sample_input.ext}
#end for
#end if
    </configfile>
  </configfiles>
  <command interpreter="python">
    scaffold_wrapper.py run \
    --samples $sample_config \
    --database $database \
    --database_name '$database.display_name'\
    --output $output \
    --database_type $database_type \
    --database_decoy_regex '$database_decoy_regex' \
    #if $thresholds.specify
    --protein_probability '$thresholds.protein_probability' \
    --peptide_probability '$thresholds.peptide_probability' \
    #end if
    #if $advanced.specify
    #if $advanced.output_driver
    --output_driver $output_driver \
    #end if
    #end if
  </command>
  <inputs>
    <param format="fasta" name="database" type="data" label="Search Database" />
    <param type="select" name="database_type" label="Database Type">
      <option value="GENERIC">Generic</option>
      <option value="ESTNR">EST/NR (NCBI)</option>
      <option value="IPI">IPI (EBI)</option>
      <option value="SWISSPROT">Swiss-Prot (SIB/EBI)</option>
      <option value="UNIPROT">UniProt/Swiss-Prot (UniProtKB)</option>
      <option value="UNIREF">UniRef/NREF (UniProt)</option>
      <option value="ENSEMBL">Ensembl (EMBL/EBI)</option>
      <option value="MSDB">MSDB (Proteomics Group)</option>
    </param>
    <param name="database_decoy_regex" type="text" label="Database Decoy Prefix" help="Regular expression describing decoys in specified FASTA databse." value="REV|RRR">
      <sanitizer>
        <valid initial="string.printable">
          <add value="|"/>
        </valid>
      </sanitizer>
    </param>
    <conditional name="sample_mode">
      <param name="mode" type="select" label="How should samples be created">
        <option value="full">Create Samples Manually</option>
        <option value="sample_per_file">Create Sample per File</option>
      </param>
      <when value="full">
        <repeat name="samples" title="Biological Sample">
          <param name="sample_name" type="text" label="Sample Name" help="Name for the scample (use only letters and numbers)." />
          <param format="t.xml,omx" name="sample_inputs" type="data" multiple="true" label="Sample Input Files" />
          <param name="mudpit" type="boolean" label="Mudpit" help="" truevalue="true" falsevalue="false" />
          <conditional name="category">
            <param name="specify" type="boolean" label="Specify Custom Category" help="" truevalue="true" falsevalue="false" />
            <when value="false" />
            <when value="true">
              <param name="name" type="text" label="Category Name" help="" />
            </when>
          </conditional>
        </repeat>
      </when>
      <when value="sample_per_file">
        <param format="t.xml,omx" name="sample_inputs" type="data" multiple="true" label="Input Files" />
      </when>
    </conditional>
    <conditional name="thresholds">
      <param name="specify" type="boolean" label="Specify Reporting Thresholds" help="" truevalue="true" falsevalue="false" />
      <when value="false" />
      <when value="true">
        <param name="protein_probability" type="float" label="Minimum Protein Probility" help="Optional value between 0.0 and 1.0." optional="true" />
        <param name="peptide_probability" type="float" label="Minimum Peptide Probility" help="Optional value between 0.0 and 1.0." optional="true" />
      </when>
    </conditional>
    <conditional name="advanced">
      <param name="specify" type="boolean" label="Specify Advanced Options" help="" truevalue="true" falsevalue="false" />
      <when value="false" />
      <when value="true">
        <param name="output_driver" type="boolean" label="Include Scaffold Driver File in Output" truevalue="true" falsevalue="false" />
        <!--
        <param name="ncbi_annotate" type="boolean" label="" truevalue="true" falsevalue="false" />
        <param name="go_annotate" type="boolean" label="" truevalue="true" falsevalue="false" />
      -->
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="xml" name="output_driver" label="Scaffold Driver for ${on_string}">
      <filter>(advanced['specify'] and advanced["output_driver"])</filter>
    </data>
    <data format="sf3" name="output" />
  </outputs>
  <requirements>
    <requirement type="package">scaffold</requirement>
  </requirements>
  <help>
**What it does**

Merges multiple protein identification search results together into a single SF3 file for viewing. A free viewer for Scaffold SF3 files can be obtained from Proteome software at http://www.proteomesoftware.com/Scaffold/Scaffold_viewer.htm.

------


**Citation**

For the underlying tool, please cite `TODO`

If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/scaffold
  </help>
</tool>