--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IDFilter.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,90 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="IDFilter" name="IDFilter" version="1.12.0">
+  <description>Filters results from protein or peptide identification engines based on different criteria.</description>
+  <macros>
+    <token name="@EXECUTABLE@">IDFilter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>IDFilter
+
+-in ${param_in}
+-out ${param_out}
+-min_length ${param_min_length}
+-max_length ${param_max_length}
+-min_charge ${param_min_charge}
+${param_var_mods}
+${param_unique}
+${param_unique_per_protein}
+${param_keep_unreferenced_protein_hits}
+${param_delete_unreferenced_peptide_hits}
+-threads \${GALAXY_SLOTS:-24} 
+-precursor:rt ${param_rt}
+-precursor:mz ${param_mz}
+${param_allow_missing}
+-score:pep ${param_pep}
+-score:prot ${param_prot}
+-thresh:pep ${param_pep}
+-thresh:prot ${param_prot}
+-whitelist:proteins ${param_proteins}
+${param_by_seq_only}
+-blacklist:peptides ${param_peptides}
+-rt:p_value ${param_p_value}
+-rt:p_value_1st_dim ${param_p_value_1st_dim}
+-mz:error ${param_error}
+-mz:unit ${param_unit}
+-best:n_peptide_hits ${param_n_peptide_hits}
+-best:n_protein_hits ${param_n_protein_hits}
+${param_strict}
+#if $adv_opts.adv_opts_selector=='advanced':
+    -best:n_to_m_peptide_hits ${adv_opts.param_n_to_m_peptide_hits}
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="idXML" optional="False" label="input file " help="(-in)"/>
+    <param name="param_min_length" type="integer" min="0" optional="True" value="0" label="Keep only peptide hits with a length greater or equal this value. Value 0 will have no filter effect." help="(-min_length)"/>
+    <param name="param_max_length" type="integer" max="0" optional="True" value="0" label="Keep only peptide hits with a length less or equal this value. Value 0 will have no filter effect. Value is overridden by min_length, i.e. if max_length &lt; min_length, max_length will be ignored." help="(-max_length)"/>
+    <param name="param_min_charge" type="integer" min="1" optional="True" value="1" label="Keep only peptide hits for tandem spectra with charge greater or equal this value." help="(-min_charge)"/>
+    <param name="param_var_mods" type="boolean" truevalue="-var_mods true" falsevalue="-var_mods false" checked="false" optional="True" label="Keep only peptide hits with variable modifications (fixed modifications from SearchParameters will be ignored)." help="(-var_mods)"/>
+    <param name="param_unique" type="boolean" truevalue="-unique true" falsevalue="-unique false" checked="false" optional="True" label="If a peptide hit occurs more than once per PSM, only one instance is kept." help="(-unique)"/>
+    <param name="param_unique_per_protein" type="boolean" truevalue="-unique_per_protein true" falsevalue="-unique_per_protein false" checked="false" optional="True" label="Only peptides matching exactly one protein are kept. Remember that isoforms count as different proteins!" help="(-unique_per_protein)"/>
+    <param name="param_keep_unreferenced_protein_hits" type="boolean" truevalue="-keep_unreferenced_protein_hits true" falsevalue="-keep_unreferenced_protein_hits false" checked="false" optional="True" label="Proteins not referenced by a peptide are retained in the idXML." help="(-keep_unreferenced_protein_hits)"/>
+    <param name="param_delete_unreferenced_peptide_hits" type="boolean" truevalue="-delete_unreferenced_peptide_hits true" falsevalue="-delete_unreferenced_peptide_hits false" checked="false" optional="True" label="Peptides not referenced by any protein are deleted in the idXML. Usually used in combination with 'score:prot' or 'thresh:prot'." help="(-delete_unreferenced_peptide_hits)"/>
+    <param name="param_rt" type="text" size="20" value=":" label="Retention time range to extract." help="(-rt)"/>
+    <param name="param_mz" type="text" size="20" value=":" label="Mass-to-charge range to extract." help="(-mz)"/>
+    <param name="param_allow_missing" type="boolean" truevalue="-precursor:allow_missing true" falsevalue="-precursor:allow_missing false" checked="false" optional="True" label="When filtering by precursor RT or m/z, keep peptide IDs with missing precursor information ('RT'/'MZ' meta values)?" help="(-allow_missing)"/>
+    <param name="param_pep" type="float" value="0.0" label="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc." help="(-pep)"/>
+    <param name="param_prot" type="float" value="0.0" label="The score which should be reached by a protein hit to be kept. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides." help="(-prot)"/>
+    <param name="param_pep" type="float" value="0.0" label="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." help="(-pep)"/>
+    <param name="param_prot" type="float" value="0.0" label="Keep a protein hit only if its score is above this fraction of the protein significance threshold. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides." help="(-prot)"/>
+    <param name="param_proteins" type="data" format="fasta" optional="True" label="filename of a FASTA file containing protein sequences.#br#All peptides that are not a substring of a sequence in this file are removed#br#All proteins whose accession is not present in this file are removed." help="(-proteins)"/>
+    <param name="param_by_seq_only" type="boolean" truevalue="-whitelist:by_seq_only true" falsevalue="-whitelist:by_seq_only false" checked="false" optional="True" label="Match peptides with FASTA file by sequence instead of accession and disable protein filtering." help="(-by_seq_only)"/>
+    <param name="param_peptides" type="data" format="idXML" optional="True" label="Peptides having the same sequence as any peptide in this file will be filtered out#br#" help="(-peptides)"/>
+    <param name="param_p_value" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict." help="(-p_value)"/>
+    <param name="param_p_value_1st_dim" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict for first dimension." help="(-p_value_1st_dim)"/>
+    <param name="param_error" type="float" value="-1.0" label="Filtering by deviation to theoretical mass (disabled for negative values)." help="(-error)"/>
+    <param name="param_unit" type="select" optional="True" value="ppm" label="Absolute or relativ error." help="(-unit)">
+      <option value="Da">Da</option>
+      <option value="ppm">ppm</option>
+    </param>
+    <param name="param_n_peptide_hits" type="integer" min="0" optional="True" value="0" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n&gt;0)." help="(-n_peptide_hits)"/>
+    <param name="param_n_protein_hits" type="integer" min="0" optional="True" value="0" label="Keep only the 'n' highest scoring protein hits (for n&gt;0)." help="(-n_protein_hits)"/>
+    <param name="param_strict" type="boolean" truevalue="-best:strict true" falsevalue="-best:strict false" checked="false" optional="True" label="Keep only the highest scoring peptide hit.#br#Similar to n_peptide_hits=1, but if there are two or more highest scoring hits, none are kept." help="(-strict)"/>
+    <expand macro="advanced_options">
+      <param name="param_n_to_m_peptide_hits" type="text" size="20" value=":" label="peptide hit rank range to extracts" help="(-n_to_m_peptide_hits)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output file " format="idXML"/>
+  </outputs>
+  <help>**What it does**
+
+Filters results from protein or peptide identification engines based on different criteria.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFilter.html
+
+@REFERENCES@
+</help>
+</tool>