--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PeptideIndexer.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,125 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="PeptideIndexer" name="PeptideIndexer" version="2.0.0">
+  <description>Refreshes the protein references for all peptide hits.</description>
+  <macros>
+    <token name="@EXECUTABLE@">PeptideIndexer</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PeptideIndexer
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_fasta:
+  -fasta $param_fasta
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_decoy_string:
+  -decoy_string     "$param_decoy_string"
+#end if
+#if $param_missing_decoy_action:
+  -missing_decoy_action
+  #if " " in str($param_missing_decoy_action):
+    "$param_missing_decoy_action"
+  #else
+    $param_missing_decoy_action
+  #end if
+#end if
+#if $param_prefix:
+  -prefix
+#end if
+#if $param_annotate_proteins:
+  -annotate_proteins
+#end if
+#if $param_write_protein_sequence:
+  -write_protein_sequence
+#end if
+#if $param_keep_unreferenced_proteins:
+  -keep_unreferenced_proteins
+#end if
+#if $param_allow_unmatched:
+  -allow_unmatched
+#end if
+#if $param_full_tolerant_search:
+  -full_tolerant_search
+#end if
+#if $param_aaa_max:
+  -aaa_max $param_aaa_max
+#end if
+#if $param_IL_equivalent:
+  -IL_equivalent
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $param_enzyme_name:
+  -enzyme:name
+  #if " " in str($param_enzyme_name):
+    "$param_enzyme_name"
+  #else
+    $param_enzyme_name
+  #end if
+#end if
+#if $param_enzyme_specificity:
+  -enzyme:specificity
+  #if " " in str($param_enzyme_specificity):
+    "$param_enzyme_specificity"
+  #else
+    $param_enzyme_specificity
+  #end if
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="idxml" optional="False" label="Input idXML file containing the identifications" help="(-in) "/>
+    <param name="param_fasta" type="data" format="fasta" optional="False" label="Input sequence database in FASTA format" help="(-fasta) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
+    <param name="param_decoy_string" type="text" size="30" value="_rev" label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" help="(-decoy_string) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_missing_decoy_action" type="select" optional="True" value="error" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message)" help="(-missing_decoy_action) ">
+      <option value="error">error</option>
+      <option value="warn">warn</option>
+    </param>
+    <param name="param_prefix" type="boolean" truevalue="-prefix" falsevalue="" checked="false" optional="True" label="If set, protein accessions in the database contain 'decoy_string' as prefix" help="(-prefix) "/>
+    <param name="param_annotate_proteins" type="boolean" truevalue="-annotate_proteins" falsevalue="" checked="false" optional="True" label="If set, add target/decoy information to proteins (as well as peptides)" help="(-annotate_proteins) "/>
+    <param name="param_write_protein_sequence" type="boolean" truevalue="-write_protein_sequence" falsevalue="" checked="false" optional="True" label="If set, the protein sequences are stored as well" help="(-write_protein_sequence) "/>
+    <param name="param_keep_unreferenced_proteins" type="boolean" truevalue="-keep_unreferenced_proteins" falsevalue="" checked="false" optional="True" label="If set, protein hits which are not referenced by any peptide are kept" help="(-keep_unreferenced_proteins) "/>
+    <param name="param_allow_unmatched" type="boolean" truevalue="-allow_unmatched" falsevalue="" checked="false" optional="True" label="If set, unmatched peptide sequences are allowed" help="(-allow_unmatched) By default (i.e. if this flag is not set) the program terminates with an error on unmatched peptides"/>
+    <param name="param_full_tolerant_search" type="boolean" truevalue="-full_tolerant_search" falsevalue="" checked="false" optional="True" label="If set, all peptide sequences are matched using tolerant search" help="(-full_tolerant_search) Thus potentially more proteins (containing ambiguous amino acids) are associated. This is much slower!"/>
+    <param name="param_aaa_max" type="integer" min="0" optional="True" value="4" label="Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein database with AAA's" help="(-aaa_max) AAA's are 'B', 'Z' and 'X'"/>
+    <param name="param_IL_equivalent" type="boolean" truevalue="-IL_equivalent" falsevalue="" checked="false" optional="True" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="(-IL_equivalent) "/>
+    <param name="param_enzyme_name" type="select" optional="True" value="Trypsin" label="Enzyme which determines valid cleavage sites -" help="(-name) e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)">
+      <option value="Trypsin">Trypsin</option>
+      <option value="none">none</option>
+    </param>
+    <param name="param_enzyme_specificity" type="select" optional="True" value="full" label="Specificity of the enzyme" help="(-specificity) &lt;br&gt;  'full': both internal cleavage sites must match. &lt;br&gt;  'semi': one of two internal cleavage sites must match. &lt;br&gt;  'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here">
+      <option value="full">full</option>
+      <option value="semi">semi</option>
+      <option value="none">none</option>
+    </param>
+    <expand macro="advanced_options">
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="idxml"/>
+  </outputs>
+  <help>**What it does**
+
+Refreshes the protein references for all peptide hits.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeptideIndexer.html</help>
+  <expand macro="references"/>
+</tool>