--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scaffold.xml	Thu Jun 20 11:07:47 2013 -0400
@@ -0,0 +1,139 @@
+<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_drirver \
+    #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_drirver" 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/galaxyp-toolshed-scaffold
+  </help>
+</tool>
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