--- a/IDFilter.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/IDFilter.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,90 +1,203 @@
-<?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
+<?xml version="1.0" encoding="UTF-8"?>
+  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+  <!--Proposed Tool Section: [ID Processing]-->
+  <tool id="IDFilter" name="IDFilter" version="2.0.0">
+    <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="references"/>
+    <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 $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_min_length:
+  -min_length $param_min_length
+#end if
+#if $param_max_length:
+  -max_length $param_max_length
+#end if
+#if $param_min_charge:
+  -min_charge $param_min_charge
+#end if
+#if $param_var_mods:
+  -var_mods
+#end if
+#if $param_unique:
+  -unique
+#end if
+#if $param_unique_per_protein:
+  -unique_per_protein
+#end if
+#if $param_keep_unreferenced_protein_hits:
+  -keep_unreferenced_protein_hits
+#end if
+#if $param_remove_decoys:
+  -remove_decoys
+#end if
+#if $param_delete_unreferenced_peptide_hits:
+  -delete_unreferenced_peptide_hits
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_precursor_rt:
+  -precursor:rt     &quot;$param_precursor_rt&quot;
+#end if
+#if $param_precursor_mz:
+  -precursor:mz     &quot;$param_precursor_mz&quot;
+#end if
+#if $param_precursor_allow_missing:
+  -precursor:allow_missing
+#end if
+#if $param_score_pep:
+  -score:pep $param_score_pep
+#end if
+#if $param_score_prot:
+  -score:prot $param_score_prot
+#end if
+#if $param_thresh_pep:
+  -thresh:pep $param_thresh_pep
+#end if
+#if $param_thresh_prot:
+  -thresh:prot $param_thresh_prot
+#end if
+#if $param_whitelist_proteins:
+  -whitelist:proteins $param_whitelist_proteins
+#end if
+#if $param_whitelist_by_seq_only:
+  -whitelist:by_seq_only
+#end if
+
+#if $rep_param_whitelist_protein_accessions:
+-whitelist:protein_accessions
+  #for token in $rep_param_whitelist_protein_accessions:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_whitelist_protein_accessions&quot;
+    #else
+      $token.param_whitelist_protein_accessions
+    #end if
+  #end for
+#end if
+#if $param_blacklist_peptides:
+  -blacklist:peptides $param_blacklist_peptides
+#end if
+#if $param_blacklist_ignore_modifications:
+  -blacklist:ignore_modifications
+#end if
+#if $param_rt_p_value:
+  -rt:p_value $param_rt_p_value
+#end if
+#if $param_rt_p_value_1st_dim:
+  -rt:p_value_1st_dim $param_rt_p_value_1st_dim
+#end if
+#if $param_mz_error:
+  -mz:error $param_mz_error
+#end if
+#if $param_mz_unit:
+  -mz:unit
+  #if &quot; &quot; in str($param_mz_unit):
+    &quot;$param_mz_unit&quot;
+  #else
+    $param_mz_unit
+  #end if
+#end if
+#if $param_best_n_peptide_hits:
+  -best:n_peptide_hits $param_best_n_peptide_hits
+#end if
+#if $param_best_n_protein_hits:
+  -best:n_protein_hits $param_best_n_protein_hits
+#end if
+#if $param_best_strict:
+  -best:strict
+#end if
 #if $adv_opts.adv_opts_selector=='advanced':
-    -best:n_to_m_peptide_hits ${adv_opts.param_n_to_m_peptide_hits}
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_best_n_to_m_peptide_hits:
+  -best:n_to_m_peptide_hits     &quot;$adv_opts.param_best_n_to_m_peptide_hits&quot;
+#end if
 #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.
+    <inputs>
+      <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param help="(-min_length) Value 0 will have no filter effect" label="Keep only peptide hits with a length greater or equal this value" min="0" name="param_min_length" optional="True" type="integer" value="0"/>
+      <param help="(-max_length) 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" label="Keep only peptide hits with a length less or equal this value" min="0" name="param_max_length" optional="True" type="integer" value="0"/>
+      <param help="(-min_charge) " label="Keep only peptide hits for tandem spectra with charge greater or equal this value" min="1" name="param_min_charge" optional="True" type="integer" value="1"/>
+      <param checked="false" falsevalue="" help="(-var_mods) " label="Keep only peptide hits with variable modifications (fixed modifications from SearchParameters will be ignored)" name="param_var_mods" optional="True" truevalue="-var_mods" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-unique) " label="If a peptide hit occurs more than once per PSM, only one instance is kept" name="param_unique" optional="True" truevalue="-unique" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-unique_per_protein) Remember that isoforms count as different proteins!" label="Only peptides matching exactly one protein are kept" name="param_unique_per_protein" optional="True" truevalue="-unique_per_protein" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-keep_unreferenced_protein_hits) " label="Proteins not referenced by a peptide are retained in the ids" name="param_keep_unreferenced_protein_hits" optional="True" truevalue="-keep_unreferenced_protein_hits" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-remove_decoys) Usually used in combination with 'delete_unreferenced_peptide_hits'" label="Remove proteins according to the information in the user parameters" name="param_remove_decoys" optional="True" truevalue="-remove_decoys" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-delete_unreferenced_peptide_hits) Usually used in combination with 'score:prot' or 'thresh:prot'" label="Peptides not referenced by any protein are deleted in the ids" name="param_delete_unreferenced_peptide_hits" optional="True" truevalue="-delete_unreferenced_peptide_hits" type="boolean"/>
+      <param help="(-rt) " label="Retention time range to extract" name="param_precursor_rt" size="30" type="text" value=":">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-mz) " label="Mass-to-charge range to extract" name="param_precursor_mz" size="30" type="text" value=":">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param checked="false" falsevalue="" help="(-allow_missing) " label="When filtering by precursor RT or m/z, keep peptide IDs with missing precursor information ('RT'/'MZ' meta values)?" name="param_precursor_allow_missing" optional="True" truevalue="-precursor:allow_missing" type="boolean"/>
+      <param help="(-pep) 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" label="The score which should be reached by a peptide hit to be kept" name="param_score_pep" type="float" value="0.0"/>
+      <param help="(-prot) Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides" label="The score which should be reached by a protein hit to be kept" name="param_score_prot" type="float" value="0.0"/>
+      <param help="(-pep) " label="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold" name="param_thresh_pep" type="float" value="0.0"/>
+      <param help="(-prot) Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides" label="Keep a protein hit only if its score is above this fraction of the protein significance threshold" name="param_thresh_prot" type="float" value="0.0"/>
+      <param format="fasta" help="(-proteins) &lt;br&gt;All peptides that are not a substring of a sequence in this file are removed &lt;br&gt;All proteins whose accession is not present in this file are removed" label="filename of a FASTA file containing protein sequences" name="param_whitelist_proteins" optional="True" type="data"/>
+      <param checked="false" falsevalue="" help="(-by_seq_only) " label="Match peptides with FASTA file by sequence instead of accession and disable protein filtering" name="param_whitelist_by_seq_only" optional="True" truevalue="-whitelist:by_seq_only" type="boolean"/>
+      <repeat min="0" name="rep_param_whitelist_protein_accessions" title="param_whitelist_protein_accessions">
+        <param help="(-protein_accessions) &lt;br&gt;Only proteins of the provided list are retained" label="All peptides that are not referencing at least one of the provided protein accession are removed" name="param_whitelist_protein_accessions" size="30" type="text">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <param format="xml" help="(-peptides) Use with blacklist:ignore_modification flag to only compare by sequence. &lt;br&gt;" label="Peptides having the same sequence and modification assignment as any peptide in this file will be filtered out" name="param_blacklist_peptides" optional="True" type="data"/>
+      <param checked="false" falsevalue="" help="(-ignore_modifications) &lt;br&gt;" label="Compare blacklisted peptides by sequence only" name="param_blacklist_ignore_modifications" optional="True" truevalue="-blacklist:ignore_modifications" type="boolean"/>
+      <param help="(-p_value) " label="Retention time filtering by the p-value predicted by RTPredict" max="1.0" min="0.0" name="param_rt_p_value" optional="True" type="float" value="0.0"/>
+      <param help="(-p_value_1st_dim) " label="Retention time filtering by the p-value predicted by RTPredict for first dimension" max="1.0" min="0.0" name="param_rt_p_value_1st_dim" optional="True" type="float" value="0.0"/>
+      <param help="(-error) " label="Filtering by deviation to theoretical mass (disabled for negative values)" name="param_mz_error" type="float" value="-1.0"/>
+      <param help="(-unit) " label="Absolute or relative erro" name="param_mz_unit" optional="True" type="select" value="ppm">
+        <option value="Da">Da</option>
+        <option value="ppm">ppm</option>
+      </param>
+      <param help="(-n_peptide_hits) " label="Keep only the 'n' highest scoring peptide hits per spectrum (for n&gt;0)" min="0" name="param_best_n_peptide_hits" optional="True" type="integer" value="0"/>
+      <param help="(-n_protein_hits) " label="Keep only the 'n' highest scoring protein hits (for n&gt;0)" min="0" name="param_best_n_protein_hits" optional="True" type="integer" value="0"/>
+      <param checked="false" falsevalue="" help="(-strict) &lt;br&gt;Similar to n_peptide_hits=1, but if there are two or more highest scoring hits, none are kept" label="Keep only the highest scoring peptide hit" name="param_best_strict" optional="True" truevalue="-best:strict" type="boolean"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+        <param help="(-n_to_m_peptide_hits) " label="peptide hit rank range to extracts" name="param_best_n_to_m_peptide_hits" size="30" type="text" value=":">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="xml" name="param_out"/>
+    </outputs>
+    <help>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>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFilter.html</help>
+  </tool>