diff FileFilter.xml @ 7:fce0d752c6c5 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

--- a/FileFilter.xml	Thu Jan 11 18:13:14 2018 -0500
+++ b/FileFilter.xml	Mon Feb 12 12:52:41 2018 -0500
@@ -1,7 +1,7 @@
 <?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.-->
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [File Handling]-->
-<tool id="FileFilter" name="FileFilter" version="2.2.0">
+<tool id="FileFilter" name="FileFilter" version="2.3.0">
   <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description>
   <macros>
     <token name="@EXECUTABLE@">FileFilter</token>
@@ -373,7 +373,7 @@
     </param>
     <param name="param_sort" display="radio" type="boolean" truevalue="-sort" falsevalue="" checked="false" optional="True" label="Sorts the output according to RT and m/z" help="(-sort) "/>
     <param name="param_peak_options_sn" type="float" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help="(-sn) "/>
-    <repeat name="rep_param_peak_options_rm_pc_charge" min="0" max="1" title="param_peak_options_rm_pc_charge">
+    <repeat name="rep_param_peak_options_rm_pc_charge" min="0" title="param_peak_options_rm_pc_charge">
       <param name="param_peak_options_rm_pc_charge" type="text" size="30" value="0" label="Remove MS(2) spectra with these precursor charges" help="(-rm_pc_charge) All spectra without precursor are kept!">
         <sanitizer>
           <valid initial="string.printable">
@@ -391,7 +391,7 @@
         </valid>
       </sanitizer>
     </param>
-    <repeat name="rep_param_peak_options_pc_mz_list" min="0" max="1" title="param_peak_options_pc_mz_list">
+    <repeat name="rep_param_peak_options_pc_mz_list" min="0" title="param_peak_options_pc_mz_list">
       <param name="param_peak_options_pc_mz_list" type="text" size="30" value="0" label="List of m/z values" help="(-pc_mz_list) If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept">
         <sanitizer>
           <valid initial="string.printable">
@@ -454,7 +454,7 @@
       <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
       <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
       <option value="Emission">Emission</option>
-      <option value="Absorbtion">Absorbtion</option>
+      <option value="Absorption">Absorption</option>
     </param>
     <param name="param_spectra_remove_activation" type="select" optional="True" label="Remove MSn scans where any of its precursors features a certain activation method" help="(-remove_activation) ">
       <option value="Collision-induced dissociation">Collision-induced dissociation</option>
@@ -503,7 +503,7 @@
       <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
       <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
       <option value="Emission">Emission</option>
-      <option value="Absorbtion">Absorbtion</option>
+      <option value="Absorption">Absorption</option>
     </param>
     <param name="param_spectra_select_activation" type="select" optional="True" label="Retain MSn scans where any of its precursors features a certain activation method" help="(-select_activation) ">
       <option value="Collision-induced dissociation">Collision-induced dissociation</option>
@@ -549,7 +549,7 @@
         </valid>
       </sanitizer>
     </param>
-    <repeat name="rep_param_consensus_map" min="0" max="1" title="param_consensus_map">
+    <repeat name="rep_param_consensus_map" min="0" title="param_consensus_map">
       <param name="param_consensus_map" type="text" size="30" value="0" label="Maps to be extracted from a consensus" help="(-map) ">
         <sanitizer>
           <valid initial="string.printable">
@@ -565,7 +565,7 @@
       <option value="true" selected="true">true</option>
     </param>
     <param name="param_consensus_blackorwhitelist_file" type="data" format="consensusxml" optional="True" label="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file! &lt;br&gt;Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options" help="(-file) &lt;br&gt;If consensus:blackorwhitelist:maps is specified, only these will be used. &lt;br&gt;"/>
-    <repeat name="rep_param_consensus_blackorwhitelist_maps" min="0" max="1" title="param_consensus_blackorwhitelist_maps">
+    <repeat name="rep_param_consensus_blackorwhitelist_maps" min="0" title="param_consensus_blackorwhitelist_maps">
       <param name="param_consensus_blackorwhitelist_maps" type="text" size="30" value="0" label="Maps used for black/white list filtering" help="(-maps) ">
         <sanitizer>
           <valid initial="string.printable">
@@ -594,7 +594,7 @@
         </valid>
       </sanitizer>
     </param>
-    <repeat name="rep_param_f_and_c_remove_meta" min="0" max="1" title="param_f_and_c_remove_meta">
+    <repeat name="rep_param_f_and_c_remove_meta" min="0" title="param_f_and_c_remove_meta">
       <param name="param_f_and_c_remove_meta" type="text" size="30" label="Expects a 3-tuple (=3 entries in the list), i.e" help="(-remove_meta) &lt;name&gt; 'lt|eq|gt' &lt;value&gt;; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!">
         <sanitizer>
           <valid initial="string.printable">
@@ -605,7 +605,7 @@
       </param>
     </repeat>
     <param name="param_id_keep_best_score_id" display="radio" type="boolean" truevalue="-id:keep_best_score_id" falsevalue="" checked="false" optional="True" label="in case of multiple peptide identifications, keep only the id with best score" help="(-keep_best_score_id) "/>
-    <repeat name="rep_param_id_sequences_whitelist" min="0" max="1" title="param_id_sequences_whitelist">
+    <repeat name="rep_param_id_sequences_whitelist" min="0" title="param_id_sequences_whitelist">
       <param name="param_id_sequences_whitelist" type="text" size="30" label="keep only features with white listed sequences," help="(-sequences_whitelist) e.g. LYSNLVER or the modification (Oxidation)">
         <sanitizer>
           <valid initial="string.printable">
@@ -615,7 +615,7 @@
         </sanitizer>
       </param>
     </repeat>
-    <repeat name="rep_param_id_accessions_whitelist" min="0" max="1" title="param_id_accessions_whitelist">
+    <repeat name="rep_param_id_accessions_whitelist" min="0" title="param_id_accessions_whitelist">
       <param name="param_id_accessions_whitelist" type="text" size="30" label="keep only features with white listed accessions," help="(-accessions_whitelist) e.g. sp|P02662|CASA1_BOVIN">
         <sanitizer>
           <valid initial="string.printable">