--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scaffold_export.xml	Thu Jun 20 11:07:47 2013 -0400
@@ -0,0 +1,75 @@
+<tool id="scaffold_export" name="Scaffold Export" version="0.1.0">
+  <description>
+    Export summary from Scaffold SF3 file.
+  </description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <command interpreter="python">
+    scaffold_wrapper.py export \
+    --sf3 $sf3_input \
+    --output $output \
+    --export_type $export.export_type \
+    ## Begin Threshold Parameters
+    #set $threshold_type = $threshold.type
+    #set $threshold_options = $threshold
+    #if $threshold_type != "none"
+    --protein_probability=$threshold_options.protein_probability \
+    --peptide_probability=$threshold_options.peptide_probability \
+    --minimum_peptide_count=$threshold_options.minimum_peptide_count \
+    #if $threshold_type != "simple"
+    $threshold_options.ignore_charge_1 \
+    $threshold_options.ignore_charge_2 \
+    $threshold_options.ignore_charge_3 \
+    $threshold_options.ignore_charge_4 \
+    --minimum_ntt=$threshold_options.minimum_ntt \
+    --minimum_peptide_length=$threshold_options.minimum_peptide_length \
+    #end if
+    #end if
+    ## End Threshold Parameters
+  </command>
+  <inputs>
+    <param format="sf3" name="sf3_input" type="data" label="Scaffold Results" />
+    <conditional name="export">
+      <param name="export_type" type="select" label="Export Format">
+        <option value="mzIdentML">MzIdentML</option>
+        <option value="protxml">ProtXML</option>
+        <option value="statistics">Stastics (tabular)</option>
+        <option value="spectrum-report">Spectrum Report (tabular)</option>
+        <option value="peptide-report">Peptide Report (tabular)</option>
+        <option value="protein-report">Protein Report (tabular)</option>
+        <option value="publication-report">Publication Report (tabular)</option>
+        <option value="isoform-report">Isoform Report (tabular)</option>
+        <option value="spectrum-counting-report">Spectrum Counting Report (tabular)</option>
+        <option value="accession-report">Accession Report (tabular)</option>
+        <option value="experiment-report">Experiment Report (tabular)</option>
+      </param>
+    </conditional>
+    <expand macro="threshold" />
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output">
+      <change_format>
+        <when input="export.export_type" value="mzIdentML" format="mzid" />
+        <when input="export.export_type" value="protxml" format="protxml" />
+      </change_format>
+    </data>
+  </outputs>
+  <requirements>
+    <requirement type="package">scaffold</requirement>
+  </requirements>
+  <help>
+**What it does**
+
+Export data out of Scaffold's binary data format (sf3) into tabular reports or XML.
+
+------
+
+
+**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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