--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FileFilter.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,252 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="FileFilter" name="FileFilter" version="1.12.0">
+  <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description>
+  <macros>
+    <token name="@EXECUTABLE@">FileFilter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>FileFilter
+
+-in ${param_in}
+-in_type ${param_in_type}
+-out ${param_out}
+-out_type ${param_out_type}
+-rt ${param_rt}
+-mz ${param_mz}
+-pc_mz ${param_pc_mz}
+-int ${param_int}
+${param_sort}
+-threads \${GALAXY_SLOTS:-24} 
+-peak_options:sn ${param_sn}
+-peak_options:rm_pc_charge ${param_rm_pc_charge}
+-peak_options:level ${param_level}
+${param_sort_peaks}
+${param_no_chromatograms}
+${param_remove_chromatograms}
+-peak_options:mz_precision ${param_mz_precision}
+-peak_options:int_precision ${param_int_precision}
+${param_indexed_file}
+-peak_options:numpress:masstime ${param_masstime}
+-peak_options:numpress:masstime_error ${param_masstime_error}
+-peak_options:numpress:intensity ${param_intensity}
+-peak_options:numpress:intensity_error ${param_intensity_error}
+${param_remove_zoom}
+-spectra:remove_mode ${param_remove_mode}
+-spectra:remove_activation ${param_remove_activation}
+-spectra:remove_collision_energy ${param_remove_collision_energy}
+-spectra:remove_isolation_window_width ${param_remove_isolation_window_width}
+${param_select_zoom}
+-spectra:select_mode ${param_select_mode}
+-spectra:select_activation ${param_select_activation}
+-spectra:select_collision_energy ${param_select_collision_energy}
+-spectra:select_isolation_window_width ${param_select_isolation_window_width}
+-spectra:select_polarity ${param_select_polarity}
+-feature:q ${param_q}
+-consensus:map ${param_map}
+${param_map_and}
+${param_blacklist}
+-consensus:blackorwhitelist:file ${param_file}
+-consensus:blackorwhitelist:maps ${param_maps}
+-consensus:blackorwhitelist:rt ${param_rt}
+-consensus:blackorwhitelist:mz ${param_mz}
+${param_use_ppm_tolerance}
+-f_and_c:charge ${param_charge}
+-f_and_c:size ${param_size}
+-f_and_c:remove_meta ${param_remove_meta}
+${param_keep_best_score_id}
+-id:sequences_whitelist ${param_sequences_whitelist}
+-id:accessions_whitelist ${param_accessions_whitelist}
+${param_remove_annotated_features}
+${param_remove_unannotated_features}
+${param_remove_unassigned_ids}
+-id:blacklist ${param_blacklist}
+-id:rt ${param_rt}
+-id:mz ${param_mz}
+${param_blacklist_imperfect}
+-algorithm:SignalToNoise:win_len ${param_win_len}
+-algorithm:SignalToNoise:bin_count ${param_bin_count}
+-algorithm:SignalToNoise:min_required_elements ${param_min_required_elements}
+#if $adv_opts.adv_opts_selector=='advanced':
+    ${adv_opts.param_remove_clashes}
+    -algorithm:SignalToNoise:max_intensity ${adv_opts.param_max_intensity}
+    -algorithm:SignalToNoise:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor}
+    -algorithm:SignalToNoise:auto_max_percentile ${adv_opts.param_auto_max_percentile}
+    -algorithm:SignalToNoise:auto_mode ${adv_opts.param_auto_mode}
+    -algorithm:SignalToNoise:noise_for_empty_window ${adv_opts.param_noise_for_empty_window}
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzML,featureXML,consensusXML" optional="False" label="Input file" help="(-in)"/>
+    <param name="param_in_type" type="select" optional="True" label="Input file type -- default: determined from file extension or content" help="(-in_type)">
+      <option value="mzML">mzML</option>
+      <option value="featureXML">featureXML</option>
+      <option value="consensusXML">consensusXML</option>
+    </param>
+    <param name="param_out_type" type="select" optional="True" label="Output file type -- default: determined from file extension or content" help="(-out_type)">
+      <option value="mzML">mzML</option>
+      <option value="featureXML">featureXML</option>
+      <option value="consensusXML">consensusXML</option>
+    </param>
+    <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="m/z range to extract (applies to ALL ms levels!)" help="(-mz)"/>
+    <param name="param_pc_mz" type="text" size="20" value=":" label="MSn (n&gt;=2) precursor filtering according to their m/z value. Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag." help="(-pc_mz)"/>
+    <param name="param_int" type="text" size="20" value=":" label="Intensity range to extract" help="(-int)"/>
+    <param name="param_sort" type="boolean" truevalue="-sort true" falsevalue="-sort false" checked="false" optional="True" label="Sorts the output according to RT and m/z." help="(-sort)"/>
+    <param name="param_sn" type="float" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help="(-sn)"/>
+    <param name="param_rm_pc_charge" type="text" size="20" value="0" label="Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!" help="(-rm_pc_charge)"/>
+    <param name="param_level" type="text" size="20" value="1 2 3" label="MS levels to extract" help="(-level)"/>
+    <param name="param_sort_peaks" type="boolean" truevalue="-peak_options:sort_peaks true" falsevalue="-peak_options:sort_peaks false" checked="false" optional="True" label="Sorts the peaks according to m/z" help="(-sort_peaks)"/>
+    <param name="param_no_chromatograms" type="boolean" truevalue="-peak_options:no_chromatograms true" falsevalue="-peak_options:no_chromatograms false" checked="false" optional="True" label="No conversion to space-saving real chromatograms, e.g. from SRM scans" help="(-no_chromatograms)"/>
+    <param name="param_remove_chromatograms" type="boolean" truevalue="-peak_options:remove_chromatograms true" falsevalue="-peak_options:remove_chromatograms false" checked="false" optional="True" label="Removes chromatograms stored in a file" help="(-remove_chromatograms)"/>
+    <param name="param_mz_precision" type="select" optional="True" value="64" label="Store base64 encoded m/z data using 32 or 64 bit precision" help="(-mz_precision)">
+      <option value="32">32</option>
+      <option value="64">64</option>
+    </param>
+    <param name="param_int_precision" type="select" optional="True" value="32" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="(-int_precision)">
+      <option value="32">32</option>
+      <option value="64">64</option>
+    </param>
+    <param name="param_indexed_file" type="boolean" truevalue="-peak_options:indexed_file true" falsevalue="-peak_options:indexed_file false" checked="false" optional="True" label="Whether to add an index to the file when writing" help="(-indexed_file)"/>
+    <param name="param_masstime" type="select" optional="True" value="none" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="(-masstime)">
+      <option value="none">none</option>
+      <option value="linear">linear</option>
+      <option value="pic">pic</option>
+      <option value="slof">slof</option>
+    </param>
+    <param name="param_masstime_error" type="float" value="0.0001" label="Maximal allowable error in m/z or rt dimension (set to 0.5 for pic)" help="(-masstime_error)"/>
+    <param name="param_intensity" type="select" optional="True" value="none" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="(-intensity)">
+      <option value="none">none</option>
+      <option value="linear">linear</option>
+      <option value="pic">pic</option>
+      <option value="slof">slof</option>
+    </param>
+    <param name="param_intensity_error" type="float" value="0.0001" label="Maximal allowable error in intensity dimension (set to 0.5 for pic)" help="(-intensity_error)"/>
+    <param name="param_remove_zoom" type="boolean" truevalue="-spectra:remove_zoom true" falsevalue="-spectra:remove_zoom false" checked="false" optional="True" label="Remove zoom (enhanced resolution) scans" help="(-remove_zoom)"/>
+    <param name="param_remove_mode" type="select" optional="True" label="Remove scans by scan mode" help="(-remove_mode)">
+      <option value="Unknown">Unknown</option>
+      <option value="MassSpectrum">MassSpectrum</option>
+      <option value="MS1Spectrum">MS1Spectrum</option>
+      <option value="MSnSpectrum">MSnSpectrum</option>
+      <option value="SelectedIonMonitoring">SelectedIonMonitoring</option>
+      <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option>
+      <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option>
+      <option value="ConstantNeutralGain">ConstantNeutralGain</option>
+      <option value="ConstantNeutralLoss">ConstantNeutralLoss</option>
+      <option value="Precursor">Precursor</option>
+      <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option>
+      <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
+      <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
+      <option value="Emission">Emission</option>
+      <option value="Absorbtion">Absorbtion</option>
+    </param>
+    <param name="param_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>
+      <option value="Post-source decay">Post-source decay</option>
+      <option value="Plasma desorption">Plasma desorption</option>
+      <option value="Surface-induced dissociation">Surface-induced dissociation</option>
+      <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
+      <option value="Electron capture dissociation">Electron capture dissociation</option>
+      <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
+      <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
+      <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
+      <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
+      <option value="Photodissociation">Photodissociation</option>
+      <option value="Electron transfer dissociation">Electron transfer dissociation</option>
+      <option value="Pulsed q dissociation">Pulsed q dissociation</option>
+    </param>
+    <param name="param_remove_collision_energy" type="text" size="20" value=":" label="Remove MSn scans with a collision energy in the given interval" help="(-remove_collision_energy)"/>
+    <param name="param_remove_isolation_window_width" type="text" size="20" value=":" label="Remove MSn scans whose isolation window width is in the given interval" help="(-remove_isolation_window_width)"/>
+    <param name="param_select_zoom" type="boolean" truevalue="-spectra:select_zoom true" falsevalue="-spectra:select_zoom false" checked="false" optional="True" label="Select zoom (enhanced resolution) scans" help="(-select_zoom)"/>
+    <param name="param_select_mode" type="select" optional="True" label="Selects scans by scan mode#br#" help="(-select_mode)">
+      <option value="Unknown">Unknown</option>
+      <option value="MassSpectrum">MassSpectrum</option>
+      <option value="MS1Spectrum">MS1Spectrum</option>
+      <option value="MSnSpectrum">MSnSpectrum</option>
+      <option value="SelectedIonMonitoring">SelectedIonMonitoring</option>
+      <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option>
+      <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option>
+      <option value="ConstantNeutralGain">ConstantNeutralGain</option>
+      <option value="ConstantNeutralLoss">ConstantNeutralLoss</option>
+      <option value="Precursor">Precursor</option>
+      <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option>
+      <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
+      <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
+      <option value="Emission">Emission</option>
+      <option value="Absorbtion">Absorbtion</option>
+    </param>
+    <param name="param_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>
+      <option value="Post-source decay">Post-source decay</option>
+      <option value="Plasma desorption">Plasma desorption</option>
+      <option value="Surface-induced dissociation">Surface-induced dissociation</option>
+      <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
+      <option value="Electron capture dissociation">Electron capture dissociation</option>
+      <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
+      <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
+      <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
+      <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
+      <option value="Photodissociation">Photodissociation</option>
+      <option value="Electron transfer dissociation">Electron transfer dissociation</option>
+      <option value="Pulsed q dissociation">Pulsed q dissociation</option>
+    </param>
+    <param name="param_select_collision_energy" type="text" size="20" value=":" label="Select MSn scans with a collision energy in the given interval" help="(-select_collision_energy)"/>
+    <param name="param_select_isolation_window_width" type="text" size="20" value=":" label="Select MSn scans whose isolation window width is in the given interval" help="(-select_isolation_window_width)"/>
+    <param name="param_select_polarity" type="select" optional="True" label="Retain MSn scans with a certain scan polarity" help="(-select_polarity)">
+      <option value="unknown">unknown</option>
+      <option value="positive">positive</option>
+      <option value="negative">negative</option>
+    </param>
+    <param name="param_q" type="text" size="20" value=":" label="Overall quality range to extract [0:1]" help="(-q)"/>
+    <param name="param_map" type="text" size="20" value="0" label="Maps to be extracted from a consensus" help="(-map)"/>
+    <param name="param_map_and" type="boolean" truevalue="-consensus:map_and true" falsevalue="-consensus:map_and false" checked="false" optional="True" label="Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map')" help="(-map_and)"/>
+    <param name="param_blacklist" type="boolean" truevalue="-consensus:blackorwhitelist:blacklist true" falsevalue="-consensus:blackorwhitelist:blacklist false" checked="true" optional="True" label="True: remove matched MS2. False: retain matched MS2 spectra. Other levels are kept" help="(-blacklist)"/>
+    <param name="param_file" type="data" format="consensusXML" optional="True" label="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file!#br#Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options.#br#If consensus:blackorwhitelist:maps is specified, only these will be used.#br#" help="(-file)"/>
+    <param name="param_maps" type="text" size="20" value="0" label="Maps used for black/white list filtering" help="(-maps)"/>
+    <param name="param_rt" type="float" min="0.0" optional="True" value="60.0" label="Retention tolerance [s] for precursor to consensus feature position" help="(-rt)"/>
+    <param name="param_mz" type="float" min="0.0" optional="True" value="0.01" label="m/z tolerance [Th] for precursor to consensus feature position" help="(-mz)"/>
+    <param name="param_use_ppm_tolerance" type="boolean" truevalue="-consensus:blackorwhitelist:use_ppm_tolerance true" falsevalue="-consensus:blackorwhitelist:use_ppm_tolerance false" checked="false" optional="True" label="If ppm tolerance should be used. Otherwise Da are used." help="(-use_ppm_tolerance)"/>
+    <param name="param_charge" type="text" size="20" value=":" label="Charge range to extract" help="(-charge)"/>
+    <param name="param_size" type="text" size="20" value=":" label="Size range to extract" help="(-size)"/>
+    <param name="param_remove_meta" type="text" size="20" label="Expects a 3-tuple (=3 entries in the list), i.e. &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!)!" help="(-remove_meta)"/>
+    <param name="param_keep_best_score_id" type="boolean" truevalue="-id:keep_best_score_id true" falsevalue="-id:keep_best_score_id false" checked="false" optional="True" label="in case of multiple peptide identifications, keep only the id with best score" help="(-keep_best_score_id)"/>
+    <param name="param_sequences_whitelist" type="text" size="20" label="keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)" help="(-sequences_whitelist)"/>
+    <param name="param_accessions_whitelist" type="text" size="20" label="keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN" help="(-accessions_whitelist)"/>
+    <param name="param_remove_annotated_features" type="boolean" truevalue="-id:remove_annotated_features true" falsevalue="-id:remove_annotated_features false" checked="false" optional="True" label="Remove features with annotations" help="(-remove_annotated_features)"/>
+    <param name="param_remove_unannotated_features" type="boolean" truevalue="-id:remove_unannotated_features true" falsevalue="-id:remove_unannotated_features false" checked="false" optional="True" label="Remove features without annotations" help="(-remove_unannotated_features)"/>
+    <param name="param_remove_unassigned_ids" type="boolean" truevalue="-id:remove_unassigned_ids true" falsevalue="-id:remove_unassigned_ids false" checked="false" optional="True" label="Remove unassigned peptide identifications" help="(-remove_unassigned_ids)"/>
+    <param name="param_blacklist" type="data" format="idXML" optional="True" label="Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file!#br#Matching tolerances are taken from 'id:rt' and 'id:mz' options.#br#This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:blacklist_imperfect' to allow for mismatches." help="(-blacklist)"/>
+    <param name="param_rt" type="float" min="0.0" optional="True" value="0.1" label="Retention tolerance [s] for precursor to id position" help="(-rt)"/>
+    <param name="param_mz" type="float" min="0.0" optional="True" value="0.001" label="m/z tolerance [Th] for precursor to id position" help="(-mz)"/>
+    <param name="param_blacklist_imperfect" type="boolean" truevalue="-id:blacklist_imperfect true" falsevalue="-id:blacklist_imperfect false" checked="false" optional="True" label="Allow for mismatching precursor positions (see 'id:blacklist')" help="(-blacklist_imperfect)"/>
+    <param name="param_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len)"/>
+    <param name="param_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count)"/>
+    <param name="param_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements)"/>
+    <expand macro="advanced_options">
+      <param name="param_remove_clashes" type="boolean" truevalue="-id:remove_clashes true" falsevalue="-id:remove_clashes false" checked="false" optional="True" label="Remove features with id clashes (different sequences mapped to one feature)" help="(-remove_clashes)"/>
+      <param name="param_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well.  If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N." help="(-max_intensity)"/>
+      <param name="param_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor)"/>
+      <param name="param_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile)"/>
+      <param name="param_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help="(-auto_mode)"/>
+      <param name="param_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="Output file" format="consensusXML">
+      <change_format>
+        <when input="param_out_type" value="mzML" format="mzML"/>
+        <when input="param_out_type" value="featureXML" format="featureXML"/>
+      </change_format>
+    </data>
+  </outputs>
+  <help>**What it does**
+
+Extracts or manipulates portions of data from peak, feature or consensus-feature files.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileFilter.html
+
+@REFERENCES@
+</help>
+</tool>