diff InclusionExclusionListCreator.xml @ 0:3d84209d3178 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/InclusionExclusionListCreator.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,107 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="1.12.0">
+  <description>Creates inclusion and/or exclusion lists.</description>
+  <macros>
+    <token name="@EXECUTABLE@">InclusionExclusionListCreator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>InclusionExclusionListCreator
+
+-include ${param_include}
+-exclude ${param_exclude}
+-out ${param_out}
+-rt_model ${param_rt_model}
+-pt_model ${param_pt_model}
+-inclusion_charges ${param_inclusion_charges}
+-inclusion_strategy ${param_inclusion_strategy}
+-exclusion_charges ${param_exclusion_charges}
+-raw_data ${param_raw_data}
+-threads \${GALAXY_SLOTS:-24} 
+-algorithm:InclusionExclusionList:missed_cleavages ${param_missed_cleavages}
+-algorithm:InclusionExclusionList:RT:unit ${param_unit}
+${param_use_relative}
+-algorithm:InclusionExclusionList:RT:window_relative ${param_window_relative}
+-algorithm:InclusionExclusionList:RT:window_absolute ${param_window_absolute}
+-algorithm:InclusionExclusionList:merge:mz_tol ${param_mz_tol}
+-algorithm:InclusionExclusionList:merge:mz_tol_unit ${param_mz_tol_unit}
+-algorithm:InclusionExclusionList:merge:rt_tol ${param_rt_tol}
+-algorithm:PrecursorSelection:ms2_spectra_per_rt_bin ${param_ms2_spectra_per_rt_bin}
+${param_exclude_overlapping_peaks}
+${param_use_dynamic_exclusion}
+-algorithm:PrecursorSelection:Exclusion:exclusion_time ${param_exclusion_time}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size ${param_max_list_size}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt ${param_min_rt}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt ${param_max_rt}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size ${param_rt_step_size}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size ${param_rt_window_size}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability ${param_min_protein_id_probability}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight ${param_min_pt_weight}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz ${param_min_mz}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz ${param_max_mz}
+${param_use_peptide_rule}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids ${param_min_peptide_ids}
+-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability ${param_min_peptide_probability}
+${param_no_intensity_normalization}
+-algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature ${param_max_number_precursors_per_feature}
+</command>
+  <inputs>
+    <param name="param_include" type="data" format="featureXML,fasta" optional="True" label="Inclusion list input file in FASTA or featureXML format." help="(-include)"/>
+    <param name="param_exclude" type="data" format="featureXML,idXML,fasta" optional="True" label="Exclusion list input file in featureXML, idXML or FASTA format." help="(-exclude)"/>
+    <param name="param_rt_model" type="data" format="txt" optional="True" label="RTModel file used for the rt prediction of peptides in FASTA files." help="(-rt_model)"/>
+    <param name="param_pt_model" type="data" format="txt" optional="True" label="PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP)." help="(-pt_model)"/>
+    <param name="param_inclusion_charges" type="text" min="1" optional="True" size="20" value="1" label="List containing the charge states to be considered for the inclusion list compounds, space separated." help="(-inclusion_charges)"/>
+    <param name="param_inclusion_strategy" type="select" optional="True" value="ALL" label="strategy to be used for selection" help="(-inclusion_strategy)">
+      <option value="FeatureBased_LP">FeatureBased_LP</option>
+      <option value="ProteinBased_LP">ProteinBased_LP</option>
+      <option value="ALL">ALL</option>
+    </param>
+    <param name="param_exclusion_charges" type="text" min="1" optional="True" size="20" value="1" label="List containing the charge states to be considered for the exclusion list compounds (for idXML and FASTA input), space separated." help="(-exclusion_charges)"/>
+    <param name="param_raw_data" type="data" format="mzML" optional="True" label="File containing the raw data (only needed for FeatureBased_LP)." help="(-raw_data)"/>
+    <param name="param_missed_cleavages" type="integer" value="0" label="Number of missed cleavages used for protein digestion.#br#" help="(-missed_cleavages)"/>
+    <param name="param_unit" type="select" optional="True" value="minutes" label="Create lists with units as seconds instead of minutes" help="(-unit)">
+      <option value="minutes">minutes</option>
+      <option value="seconds">seconds</option>
+    </param>
+    <param name="param_use_relative" type="boolean" truevalue="-algorithm:InclusionExclusionList:RT:use_relative true" falsevalue="-algorithm:InclusionExclusionList:RT:use_relative false" checked="true" optional="True" label="Use relative RT window, which depends on RT of precursor." help="(-use_relative)"/>
+    <param name="param_window_relative" type="float" min="0.0" max="10.0" optional="True" value="0.05" label="[for RT:use_relative == true] The relative factor X for the RT exclusion window, e.g. the window is calculated as [rt - rt*X, rt + rt*X]." help="(-window_relative)"/>
+    <param name="param_window_absolute" type="float" min="0.0" optional="True" value="90.0" label="[for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec], e.g. the window is calculated as [rt - X, rt + X]." help="(-window_absolute)"/>
+    <param name="param_mz_tol" type="float" min="0.0" optional="True" value="10.0" label="Two inclusion/exclusion windows are merged when they (almost) overlap in RT (see 'rt_tol') and are close in m/z by this tolerance. Unit of this is defined in 'mz_tol_unit'." help="(-mz_tol)"/>
+    <param name="param_mz_tol_unit" type="select" optional="True" value="ppm" label="Unit of 'mz_tol'" help="(-mz_tol_unit)">
+      <option value="ppm">ppm</option>
+      <option value="Da">Da</option>
+    </param>
+    <param name="param_rt_tol" type="float" min="0.0" optional="True" value="1.1" label="Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows). Two inclusion/exclusion windows are merged when they (almost) overlap in RT and are close in m/z by this tolerance (see 'mz_tol'). Unit of this param is [seconds]." help="(-rt_tol)"/>
+    <param name="param_ms2_spectra_per_rt_bin" type="integer" min="1" optional="True" value="5" label="Number of allowed MS/MS spectra in a retention time bin." help="(-ms2_spectra_per_rt_bin)"/>
+    <param name="param_exclude_overlapping_peaks" type="boolean" truevalue="-algorithm:PrecursorSelection:exclude_overlapping_peaks true" falsevalue="-algorithm:PrecursorSelection:exclude_overlapping_peaks false" checked="false" optional="True" label="If true overlapping or nearby peaks (within min_peak_distance) are excluded for selection." help="(-exclude_overlapping_peaks)"/>
+    <param name="param_use_dynamic_exclusion" type="boolean" truevalue="-algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion true" falsevalue="-algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion false" checked="false" optional="True" label="If true dynamic exclusion is applied." help="(-use_dynamic_exclusion)"/>
+    <param name="param_exclusion_time" type="float" min="0.0" optional="True" value="100.0" label="The time (in seconds) a feature is excluded." help="(-exclusion_time)"/>
+    <param name="param_max_list_size" type="integer" min="1" optional="True" value="1000" label="The maximal number of precursors in the inclusion list." help="(-max_list_size)"/>
+    <param name="param_min_rt" type="float" min="0.0" optional="True" value="960.0" label="Minimal rt in seconds." help="(-min_rt)"/>
+    <param name="param_max_rt" type="float" min="0.0" optional="True" value="3840.0" label="Maximal rt in seconds." help="(-max_rt)"/>
+    <param name="param_rt_step_size" type="float" min="1.0" optional="True" value="30.0" label="rt step size in seconds." help="(-rt_step_size)"/>
+    <param name="param_rt_window_size" type="integer" min="1" optional="True" value="100" label="rt window size in seconds." help="(-rt_window_size)"/>
+    <param name="param_min_protein_id_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Minimal protein probability for a protein to be considered identified." help="(-min_protein_id_probability)"/>
+    <param name="param_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precursor" help="(-min_pt_weight)"/>
+    <param name="param_min_mz" type="float" min="0.0" optional="True" value="500.0" label="Minimal mz to be considered in protein based LP formulation." help="(-min_mz)"/>
+    <param name="param_max_mz" type="float" min="0.0" optional="True" value="5000.0" label="Minimal mz to be considered in protein based LP formulation." help="(-max_mz)"/>
+    <param name="param_use_peptide_rule" type="boolean" truevalue="-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule true" falsevalue="-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule false" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule)"/>
+    <param name="param_min_peptide_ids" type="integer" min="1" optional="True" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help="(-min_peptide_ids)"/>
+    <param name="param_min_peptide_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help="(-min_peptide_probability)"/>
+    <param name="param_no_intensity_normalization" type="boolean" truevalue="-algorithm:PrecursorSelection:feature_based:no_intensity_normalization true" falsevalue="-algorithm:PrecursorSelection:feature_based:no_intensity_normalization false" checked="false" optional="True" label="Flag indicating if intensities shall be scaled to be in [0,1]. This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1." help="(-no_intensity_normalization)"/>
+    <param name="param_max_number_precursors_per_feature" type="integer" min="1" optional="True" value="1" label="The maximal number of precursors per feature." help="(-max_number_precursors_per_feature)"/>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="Output file (tab delimited csv file)." format="tabular"/>
+  </outputs>
+  <help>**What it does**
+
+Creates inclusion and/or exclusion lists.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html
+
+@REFERENCES@
+</help>
+</tool>