Mercurial > repos > bgruening > openms
diff 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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--- a/MapAlignerPoseClustering.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MapAlignerPoseClustering.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,92 +1,187 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="1.12.0"> - <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="stdio"/> - <expand macro="requirements"/> - <command>MapAlignerPoseClustering +<?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 --in ${param_in} --out ${param_out} --trafo_out ${param_trafo_out} --threads \${GALAXY_SLOTS:-24} --reference:file ${param_file} --reference:index ${param_index} --algorithm:max_num_peaks_considered ${param_max_num_peaks_considered} --algorithm:superimposer:mz_pair_max_distance ${param_mz_pair_max_distance} --algorithm:superimposer:num_used_points ${param_num_used_points} --algorithm:superimposer:scaling_bucket_size ${param_scaling_bucket_size} --algorithm:superimposer:shift_bucket_size ${param_shift_bucket_size} --algorithm:pairfinder:second_nearest_gap ${param_second_nearest_gap} -${param_use_identifications} -${param_ignore_charge} --algorithm:pairfinder:distance_RT:max_difference ${param_max_difference} --algorithm:pairfinder:distance_MZ:max_difference ${param_max_difference} --algorithm:pairfinder:distance_MZ:unit ${param_unit} +#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': - -algorithm:superimposer:rt_pair_distance_fraction ${adv_opts.param_rt_pair_distance_fraction} - -algorithm:superimposer:max_shift ${adv_opts.param_max_shift} - -algorithm:superimposer:max_scaling ${adv_opts.param_max_scaling} - -algorithm:superimposer:dump_buckets ${adv_opts.param_dump_buckets} - -algorithm:superimposer:dump_pairs ${adv_opts.param_dump_pairs} - -algorithm:pairfinder:distance_RT:exponent ${adv_opts.param_exponent} - -algorithm:pairfinder:distance_RT:weight ${adv_opts.param_weight} - -algorithm:pairfinder:distance_MZ:exponent ${adv_opts.param_exponent} - -algorithm:pairfinder:distance_MZ:weight ${adv_opts.param_weight} - -algorithm:pairfinder:distance_intensity:exponent ${adv_opts.param_exponent} - -algorithm:pairfinder:distance_intensity:weight ${adv_opts.param_weight} + #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 name="param_in" type="data" format="mzML,featureXML" optional="False" size="20" label="Input files separated by blanks (all must have the same file type)" help="(-in)"/> - <param name="param_file" type="data" format="mzML,featureXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file)"/> - <param name="param_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.).#br#If '0', no explicit reference is set - the algorithm will select a reference." help="(-index)"/> - <param name="param_max_num_peaks_considered" type="integer" min="-1" optional="True" value="1000" label="The maximal number of peaks/features to be considered per map. To use all, set to '-1'." help="(-max_num_peaks_considered)"/> - <param name="param_mz_pair_max_distance" type="float" min="0.0" optional="True" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing." help="(-mz_pair_max_distance)"/> - <param name="param_num_used_points" type="integer" min="-1" optional="True" value="2000" label="Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1." help="(-num_used_points)"/> - <param name="param_scaling_bucket_size" type="float" min="0.0" optional="True" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs." help="(-scaling_bucket_size)"/> - <param name="param_shift_bucket_size" type="float" min="0.0" optional="True" value="3.0" 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. A good choice for this would be about the time between consecutive MS scans." help="(-shift_bucket_size)"/> - <param name="param_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself." help="(-second_nearest_gap)"/> - <param name="param_use_identifications" type="boolean" truevalue="-algorithm:pairfinder:use_identifications true" falsevalue="-algorithm:pairfinder:use_identifications false" checked="false" optional="True" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." help="(-use_identifications)"/> - <param name="param_ignore_charge" type="boolean" truevalue="-algorithm:pairfinder:ignore_charge true" falsevalue="-algorithm:pairfinder:ignore_charge false" checked="false" optional="True" label="Compare features normally even if their charge states are different" help="(-ignore_charge)"/> - <param name="param_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Maximum allowed difference in RT in seconds" help="(-max_difference)"/> - <param name="param_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Maximum allowed difference in m/z (unit defined by 'unit')" help="(-max_difference)"/> - <param name="param_unit" type="select" optional="True" value="Da" label="Unit of the 'max_difference' parameter" help="(-unit)"> - <option value="Da">Da</option> - <option value="ppm">ppm</option> - </param> - <expand macro="advanced_options"> - <param name="param_rt_pair_distance_fraction" type="float" min="0.0" max="1.0" optional="True" value="0.1" 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). " help="(-rt_pair_distance_fraction)"/> - <param name="param_max_shift" type="float" min="0.0" optional="True" value="1000.0" label="Maximal shift which is considered during histogramming. This applies for both directions." help="(-max_shift)"/> - <param name="param_max_scaling" type="float" min="1.0" optional="True" value="2.0" label="Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this." help="(-max_scaling)"/> - <param name="param_dump_buckets" type="text" size="20" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically." help="(-dump_buckets)"/> - <param name="param_dump_pairs" type="text" size="20" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically." help="(-dump_pairs)"/> - <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/> - <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="RT distances are weighted by this factor" help="(-weight)"/> - <param name="param_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/> - <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="m/z distances are weighted by this factor" help="(-weight)"/> - <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/> - <param name="param_weight" type="float" min="0.0" optional="True" value="0.0" label="Distances based on relative intensity are weighted by this factor" help="(-weight)"/> - </expand> - </inputs> - <outputs> - <data name="param_out" label="Output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together." format="featureXML"> - <change_format> - <when input="param_out_type" value="mzML" format="mzML"/> - </change_format> - </data> - <data name="param_trafo_out" label="Transformation output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together." format="data"/> - </outputs> - <help>**What it does** - -Corrects retention time distortions between maps using a pose clustering approach. + <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 - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help> + </tool>