--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PSM2SAM.xml	Fri Oct 02 14:14:15 2015 -0400
@@ -0,0 +1,61 @@
+<tool id="PSMtoSAM" name="PSM to SAM" version="1.3.2">
+  <description>Generate SAM files from PSMs.</description>
+  <command interpreter="Rscript --vanilla">PSM2SAM.R
+       #if str($input).strip() != "":
+          --passedPSM="$input"
+       #end if
+       #if str($scoreColumn).strip() != "":
+          --XScolumn="$scoreColumn"
+       #end if
+       #if str($optionalUserInput.exonAnno).strip() != "None":
+          --exon_anno="$optionalUserInput.exonAnno"
+       #end if
+       #if str($optionalUserInput.proteinSeq).strip() != "None":
+          --proteinseq="$optionalUserInput.proteinSeq"
+       #end if
+       #if str($optionalUserInput.proCodingSeq).strip() != "None":
+          --procodingseq="$optionalUserInput.proCodingSeq"
+       #end if
+       #if str($optionalUserInput.header).strip() != "None":
+          --header="$optionalUserInput.header"
+       #end if
+       #if str($output).strip() != "":
+          --OutputFile="$output"
+       #end if
+
+2&gt;&amp;1</command>
+  <inputs>
+    <param name="input" type="data" format="idpdb" help="An IDPicker idpDB file to convert to SAM" label="Input PSMs">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+    <param name="scoreColumn" type="text" help="The name of a PSM score to include in the SAM output (e.g. &quot;MyriMatch:mvh&quot;)" size="60" label="Score Name">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+    <section name="optionalUserInput" label="Override Default Exon Annotation and Coding Sequences">
+      <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" />
+      <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" />
+      <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" />
+      <param name="header" type="data" format="txt" help="A text file of SAM headers to include in the output file, usually corresponding to the exon and coding sequences used." label="SAM Headers" optional="true" />
+    </section>
+  </inputs>
+  <outputs>
+    <data format="sam" name="output" label="${input.name.rsplit('.',1)[0]}.sam"/>
+  </outputs>
+  <!--<tests>
+    <test>
+      <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB.gz" />
+      <param name="scoreColumn" value="Myrimatch:MVH" />
+      <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" />
+    </test>
+    <test>
+      <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB.gz" />
+      <param name="scoreColumn" value="Myrimatch:MVH" />
+      <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" />
+    </test>
+  </tests>-->
+  <help>
+**Description**
+
+Generate SAM files from confident peptide-spectrum-matches (PSMs).
+</help>
+</tool>
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