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view MapAlignerPoseClustering.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
| author | bgruening |
|---|---|
| date | Wed, 27 Jan 2016 10:06:49 -0500 |
| parents | 3d84209d3178 |
| children |
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<?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: [Map Alignment]--> <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.0.0"> <description>Corrects retention time distortions between maps using a pose clustering approach.</description> <macros> <token name="@EXECUTABLE@">MapAlignerPoseClustering</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>MapAlignerPoseClustering -in #for token in $param_in: $token #end for #if $rep_param_out: -out #for token in $rep_param_out: #if " " in str(token): "$token.param_out" #else $token.param_out #end if #end for #end if #if $rep_param_trafo_out: -trafo_out #for token in $rep_param_trafo_out: #if " " in str(token): "$token.param_trafo_out" #else $token.param_trafo_out #end if #end for #end if -threads \${GALAXY_SLOTS:-24} #if $param_reference_file: -reference:file $param_reference_file #end if #if $param_reference_index: -reference:index $param_reference_index #end if #if $param_algorithm_max_num_peaks_considered: -algorithm:max_num_peaks_considered $param_algorithm_max_num_peaks_considered #end if #if $param_algorithm_superimposer_mz_pair_max_distance: -algorithm:superimposer:mz_pair_max_distance $param_algorithm_superimposer_mz_pair_max_distance #end if #if $param_algorithm_superimposer_num_used_points: -algorithm:superimposer:num_used_points $param_algorithm_superimposer_num_used_points #end if #if $param_algorithm_superimposer_scaling_bucket_size: -algorithm:superimposer:scaling_bucket_size $param_algorithm_superimposer_scaling_bucket_size #end if #if $param_algorithm_superimposer_shift_bucket_size: -algorithm:superimposer:shift_bucket_size $param_algorithm_superimposer_shift_bucket_size #end if #if $param_algorithm_pairfinder_second_nearest_gap: -algorithm:pairfinder:second_nearest_gap $param_algorithm_pairfinder_second_nearest_gap #end if #if $param_algorithm_pairfinder_use_identifications: -algorithm:pairfinder:use_identifications #end if #if $param_algorithm_pairfinder_ignore_charge: -algorithm:pairfinder:ignore_charge #end if #if $param_algorithm_pairfinder_distance_RT_max_difference: -algorithm:pairfinder:distance_RT:max_difference $param_algorithm_pairfinder_distance_RT_max_difference #end if #if $param_algorithm_pairfinder_distance_MZ_max_difference: -algorithm:pairfinder:distance_MZ:max_difference $param_algorithm_pairfinder_distance_MZ_max_difference #end if #if $param_algorithm_pairfinder_distance_MZ_unit: -algorithm:pairfinder:distance_MZ:unit #if " " in str($param_algorithm_pairfinder_distance_MZ_unit): "$param_algorithm_pairfinder_distance_MZ_unit" #else $param_algorithm_pairfinder_distance_MZ_unit #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction: -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction #end if #if $adv_opts.param_algorithm_superimposer_max_shift: -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift #end if #if $adv_opts.param_algorithm_superimposer_max_scaling: -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling #end if #if $adv_opts.param_algorithm_superimposer_dump_buckets: -algorithm:superimposer:dump_buckets "$adv_opts.param_algorithm_superimposer_dump_buckets" #end if #if $adv_opts.param_algorithm_superimposer_dump_pairs: -algorithm:superimposer:dump_pairs "$adv_opts.param_algorithm_superimposer_dump_pairs" #end if #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent: -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent #end if #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight: -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight #end if #if $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent: -algorithm:pairfinder:distance_MZ:exponent $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent #end if #if $adv_opts.param_algorithm_pairfinder_distance_MZ_weight: -algorithm:pairfinder:distance_MZ:weight $adv_opts.param_algorithm_pairfinder_distance_MZ_weight #end if #if $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent: -algorithm:pairfinder:distance_intensity:exponent $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent #end if #if $adv_opts.param_algorithm_pairfinder_distance_intensity_weight: -algorithm:pairfinder:distance_intensity:weight $adv_opts.param_algorithm_pairfinder_distance_intensity_weight #end if #end if </command> <inputs> <param format="xml,mzml" help="(-in) " label="Input files to align (all must have the same file type)" multiple="true" name="param_in" optional="False" size="30" type="data"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param format="xml,mzml" help="(-file) " label="File to use as reference (same file format as input files required)" name="param_reference_file" optional="True" type="data"/> <param help="(-index) <br>If '0', no explicit reference is set - the algorithm will select a reference" label="Use one of the input files as reference ('1' for the first file, etc.)" min="0" name="param_reference_index" optional="True" type="integer" value="0"/> <param help="(-max_num_peaks_considered) To use all, set to '-1'" label="The maximal number of peaks/features to be considered per map" min="-1" name="param_algorithm_max_num_peaks_considered" optional="True" type="integer" value="1000"/> <param help="(-mz_pair_max_distance) This condition applies to the pairs considered in hashing" label="Maximum of m/z deviation of corresponding elements in different maps" min="0.0" name="param_algorithm_superimposer_mz_pair_max_distance" optional="True" type="float" value="0.5"/> <param help="(-num_used_points) Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1" label="Maximum number of elements considered in each map (selected by intensity)" min="-1" name="param_algorithm_superimposer_num_used_points" optional="True" type="integer" value="2000"/> <param help="(-scaling_bucket_size) A good choice for this would be a bit smaller than the error you would expect from repeated runs" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" min="0.0" name="param_algorithm_superimposer_scaling_bucket_size" optional="True" type="float" value="0.005"/> <param help="(-shift_bucket_size) A good choice for this would be about the time between consecutive MS scans" label="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering" min="0.0" name="param_algorithm_superimposer_shift_bucket_size" optional="True" type="float" value="3.0"/> <param help="(-second_nearest_gap) " label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" min="1.0" name="param_algorithm_pairfinder_second_nearest_gap" optional="True" type="float" value="2.0"/> <param checked="false" falsevalue="" help="(-use_identifications) " label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" name="param_algorithm_pairfinder_use_identifications" optional="True" truevalue="-algorithm:pairfinder:use_identifications" type="boolean"/> <param checked="false" falsevalue="" help="(-ignore_charge) " label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" name="param_algorithm_pairfinder_ignore_charge" optional="True" truevalue="-algorithm:pairfinder:ignore_charge" type="boolean"/> <param help="(-max_difference) " label="Never pair features with a larger RT distance (in seconds)" min="0.0" name="param_algorithm_pairfinder_distance_RT_max_difference" optional="True" type="float" value="100.0"/> <param help="(-max_difference) " label="Never pair features with larger m/z distance (unit defined by 'unit')" min="0.0" name="param_algorithm_pairfinder_distance_MZ_max_difference" optional="True" type="float" value="0.3"/> <param help="(-unit) " label="Unit of the 'max_difference' paramete" name="param_algorithm_pairfinder_distance_MZ_unit" optional="True" type="select" value="Da"> <option value="Da">Da</option> <option value="ppm">ppm</option> </param> <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="(-rt_pair_distance_fraction) " label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min)" max="1.0" min="0.0" name="param_algorithm_superimposer_rt_pair_distance_fraction" optional="True" type="float" value="0.1"/> <param help="(-max_shift) This applies for both directions" label="Maximal shift which is considered during histogramming (in seconds)" min="0.0" name="param_algorithm_superimposer_max_shift" optional="True" type="float" value="1000.0"/> <param help="(-max_scaling) The minimal scaling is the reciprocal of this" label="Maximal scaling which is considered during histogramming" min="1.0" name="param_algorithm_superimposer_max_scaling" optional="True" type="float" value="2.0"/> <param help="(-dump_buckets) A serial number for each invocation will be appended automatically" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" name="param_algorithm_superimposer_dump_buckets" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-dump_pairs) A serial number for each invocation will be appended automatically" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" name="param_algorithm_superimposer_dump_pairs" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-exponent) " label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_pairfinder_distance_RT_exponent" optional="True" type="float" value="1.0"/> <param help="(-weight) " label="Final RT distances are weighted by this facto" min="0.0" name="param_algorithm_pairfinder_distance_RT_weight" optional="True" type="float" value="1.0"/> <param help="(-exponent) " label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_pairfinder_distance_MZ_exponent" optional="True" type="float" value="2.0"/> <param help="(-weight) " label="Final m/z distances are weighted by this facto" min="0.0" name="param_algorithm_pairfinder_distance_MZ_weight" optional="True" type="float" value="1.0"/> <param help="(-exponent) " label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_pairfinder_distance_intensity_exponent" optional="True" type="float" value="1.0"/> <param help="(-weight) " label="Final intensity distances are weighted by this facto" min="0.0" name="param_algorithm_pairfinder_distance_intensity_weight" optional="True" type="float" value="0.0"/> </expand> </inputs> <outputs> <data format="input" metadata_source="param_in" name="param_out"/> <data format="trafoxml" name="param_trafo_out"/> </outputs> <help>Corrects retention time distortions between maps using a pose clustering approach. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help> </tool>