--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protxml_to_gff.xml	Tue Oct 20 20:36:03 2015 -0400
@@ -0,0 +1,120 @@
+<tool id="protxml_to_gff" name="Proteomics to GFF" version="1.1.0">
+    <description>Export Proteomics Data to GFF</description>
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+        <requirement type="package" version="2.2.29">blast+</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"   level="fatal"   description="Failure" />
+    </stdio>
+    <command>
+        protxml_to_gff.rb $protxml_file 
+            #if $database.source_select=="built_in":
+                -d $database.dbkey
+            #else 
+                -d $database.fasta_file
+            #end if
+            -c $gene_file
+            #if str( $gffidpattern ):
+                --gff-idregex='$gffidpattern'
+            #end if
+
+            #if str( $genomeidpattern ):
+                --genome-idregex='$genomeidpattern'
+            #end if
+
+            #if str( $ignorepattern ):
+                --ignore-regex='$ignorepattern'
+            #end if
+            
+            --threshold=$peptide_threshold
+            --prot-threshold=$prot_threshold
+            $stack_charges
+            -o $output
+    </command>
+    <inputs>
+        <conditional name="database">
+            <param name="source_select" type="select" label="Database source used for Proteomics Searches" help="Database should be an amino acid fasta file with entry id's that can be parsed to obtain contig or scaffold ids referenced in your gff file">
+                <option value="input_ref">Your Upload File</option>
+                <option value="built_in">Built-In</option>
+            </param>
+            <when value="built_in">
+                <param name="dbkey" type="select" format="text" >
+                    <label>Database</label>
+                    <options from_file="pepxml_databases.loc">
+                        <column name="name" index="0" />
+                        <column name="value" index="2" />
+                    </options>
+                </param>
+            </when>
+            <when value="input_ref">
+                <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
+            </when>
+        </conditional>
+        <param name="protxml_file" type="data" format="protxml" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/>
+        <param name="gene_file" type="data" format="gff3" multiple="false" label="Protein coordinates" help="A gff3 file with coordinates for all protein entries used for proteomics searches. Coordinates should correspond to entries in the genome fasta file"/>
+        <param name="peptide_threshold" label="Peptide Probability Threshold" type="float" value="0.95" min="0" max="1" help="Only peptides within accepted proteins and passing this threshold will appear in the output"/>
+        <param name="prot_threshold" label="Protein Probability Threshold" type="float" value="0.99" min="0" max="1" help="Only peptides within proteins passing this threshold will appear in the output"/>
+        <param name="stack_charges" value="false" type="boolean" label="Peptides with different charges get separate gff entries" help="" truevalue="--stack-charge-states" falsevalue="" />
+        <param name="gffidpattern" size="40" type="text" value="lcl\|([^ ]*)" label="gff id regex" help="Regex with capture group for parsing gff ids from protein ids">
+            <sanitizer>
+            <valid initial="string.printable">
+             <remove value="&apos;"/>
+            </valid>
+            <mapping initial="none">
+              <add source="&apos;" target="__sq__"/>
+            </mapping>
+              </sanitizer>
+        </param>
+
+        <param name="genomeidpattern" size="40" type="text" label="genome id regex" help="Regex with capture group for parsing genomic ids from protein ids">
+            <sanitizer>
+            <valid initial="string.printable">
+             <remove value="&apos;"/>
+            </valid>
+            <mapping initial="none">
+              <add source="&apos;" target="__sq__"/>
+            </mapping>
+              </sanitizer>
+        </param>        
+
+        <param name="ignorepattern" size="40" type="text" label="ignore regex" help="Regex to match protein ids that we should ignore completely">
+            <sanitizer>
+            <valid initial="string.printable">
+             <remove value="&apos;"/>
+            </valid>
+            <mapping initial="none">
+              <add source="&apos;" target="__sq__"/>
+            </mapping>
+              </sanitizer>
+        </param>        
+
+
+
+    </inputs>
+    <outputs>
+        <data format="gff3" name="output" />
+    </outputs>
+    <tests>
+      <test>
+          <param name="source_select" value="input_ref"/>
+          <param name="fasta_file" value="small_prot.fasta" format="fasta"/>
+
+          <param name="protxml_file" value="small.prot.xml" format="protxml"/>
+          <param name="gene_file" value="small_combined.gff" format="gff3"/>
+          <output name="output" format="gff3">
+              <assert_contents>
+                  <has_text text="polypeptide" />
+              </assert_contents>
+          </output>
+      </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Exports peptides and proteins to gff
+
+    </help>
+</tool>