Mercurial > repos > galaxyp > openms_mapalignerposeclustering
comparison MapAlignerPoseClustering.xml @ 2:304c13ce9577 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author | galaxyp |
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date | Mon, 12 Feb 2018 12:57:02 -0500 |
parents | 40ca4302e603 |
children | e86e83ac0cd3 |
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1:40ca4302e603 | 2:304c13ce9577 |
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1 <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.2.0"> | 1 <?xml version='1.0' encoding='UTF-8'?> |
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> | |
3 <!--Proposed Tool Section: [Map Alignment]--> | |
4 <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.3.0"> | |
2 <description>Corrects retention time distortions between maps using a pose clustering approach.</description> | 5 <description>Corrects retention time distortions between maps using a pose clustering approach.</description> |
3 <macros> | 6 <macros> |
4 <token name="@EXECUTABLE@">MapAlignerPoseClustering</token> | 7 <token name="@EXECUTABLE@">MapAlignerPoseClustering</token> |
5 <import>macros.xml</import> | 8 <import>macros.xml</import> |
6 </macros> | 9 </macros> |
10 <expand macro="references"/> | |
7 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
8 <expand macro="requirements"/> | 12 <expand macro="requirements"/> |
9 <command><![CDATA[ | 13 <command><![CDATA[ |
10 | 14 |
11 mkdir -p ./results_trafoxml ./results_out && | 15 mkdir -p ./results_trafoxml ./results_out && |
23 | 27 |
24 -trafo_out | 28 -trafo_out |
25 #for $counter,$infile in enumerate($param_in): | 29 #for $counter,$infile in enumerate($param_in): |
26 ./results_trafoxml/${infile.element_identifier}.trafoxml | 30 ./results_trafoxml/${infile.element_identifier}.trafoxml |
27 #end for | 31 #end for |
28 | |
29 -threads "\${GALAXY_SLOTS:-1}" | |
30 | 32 |
31 #if $param_reference_file: | 33 #if $param_reference_file: |
32 -reference:file $param_reference_file | 34 -reference:file $param_reference_file |
33 #end if | 35 #end if |
34 #if $param_reference_index: | 36 #if $param_reference_index: |
71 #else | 73 #else |
72 $param_algorithm_pairfinder_distance_MZ_unit | 74 $param_algorithm_pairfinder_distance_MZ_unit |
73 #end if | 75 #end if |
74 #end if | 76 #end if |
75 #if $adv_opts.adv_opts_selector=='advanced': | 77 #if $adv_opts.adv_opts_selector=='advanced': |
76 | 78 #if $adv_opts.param_force: |
79 -force | |
80 #end if | |
77 #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction: | 81 #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction: |
78 -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction | 82 -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction |
79 #end if | 83 #end if |
80 #if $adv_opts.param_algorithm_superimposer_max_shift: | 84 #if $adv_opts.param_algorithm_superimposer_max_shift: |
81 -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift | 85 -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift |
82 #end if | 86 #end if |
83 #if $adv_opts.param_algorithm_superimposer_max_scaling: | 87 #if $adv_opts.param_algorithm_superimposer_max_scaling: |
84 -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling | 88 -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling |
85 #end if | 89 #end if |
86 | 90 #if $adv_opts.param_algorithm_superimposer_dump_buckets: |
87 #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent: | 91 -algorithm:superimposer:dump_buckets "$adv_opts.param_algorithm_superimposer_dump_buckets" |
92 #end if | |
93 #if $adv_opts.param_algorithm_superimposer_dump_pairs: | |
94 -algorithm:superimposer:dump_pairs "$adv_opts.param_algorithm_superimposer_dump_pairs" | |
95 #end if | |
96 #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent: | |
88 -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent | 97 -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent |
89 #end if | 98 #end if |
90 #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight: | 99 #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight: |
91 -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight | 100 -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight |
92 #end if | 101 #end if |
109 #else | 118 #else |
110 $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform | 119 $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform |
111 #end if | 120 #end if |
112 #end if | 121 #end if |
113 #end if | 122 #end if |
114 | |
115 ]]> | 123 ]]> |
116 </command> | 124 </command> |
117 <inputs> | 125 <inputs> |
118 <param name="param_in" type="data" format="mzML,featureXML" multiple="true" label="Input files to align (all must have the same file type)" help="(-in) "/> | 126 <param name="param_in" type="data" format="mzML,featureXML" multiple="true" label="Input files to align (all must have the same file type)" help="(-in) "/> |
119 <param name="param_reference_file" type="data" format="mzML,featureXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/> | 127 <param name="param_reference_file" type="data" format="mzML,featureXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/> |
131 <param name="param_algorithm_pairfinder_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) "> | 139 <param name="param_algorithm_pairfinder_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) "> |
132 <option value="Da" selected="true">Da</option> | 140 <option value="Da" selected="true">Da</option> |
133 <option value="ppm">ppm</option> | 141 <option value="ppm">ppm</option> |
134 </param> | 142 </param> |
135 <expand macro="advanced_options"> | 143 <expand macro="advanced_options"> |
144 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
136 <param name="param_algorithm_superimposer_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) "/> | 145 <param name="param_algorithm_superimposer_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) "/> |
137 <param name="param_algorithm_superimposer_max_shift" type="float" min="0.0" optional="True" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="(-max_shift) This applies for both directions"/> | 146 <param name="param_algorithm_superimposer_max_shift" type="float" min="0.0" optional="True" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="(-max_shift) This applies for both directions"/> |
138 <param name="param_algorithm_superimposer_max_scaling" type="float" min="1.0" optional="True" value="2.0" label="Maximal scaling which is considered during histogramming" help="(-max_scaling) The minimal scaling is the reciprocal of this"/> | 147 <param name="param_algorithm_superimposer_max_scaling" type="float" min="1.0" optional="True" value="2.0" label="Maximal scaling which is considered during histogramming" help="(-max_scaling) The minimal scaling is the reciprocal of this"/> |
148 <param name="param_algorithm_superimposer_dump_buckets" type="text" size="30" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="(-dump_buckets) A serial number for each invocation will be appended automatically"> | |
149 <sanitizer> | |
150 <valid initial="string.printable"> | |
151 <remove value="'"/> | |
152 <remove value="""/> | |
153 </valid> | |
154 </sanitizer> | |
155 </param> | |
156 <param name="param_algorithm_superimposer_dump_pairs" type="text" size="30" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" help="(-dump_pairs) A serial number for each invocation will be appended automatically"> | |
157 <sanitizer> | |
158 <valid initial="string.printable"> | |
159 <remove value="'"/> | |
160 <remove value="""/> | |
161 </valid> | |
162 </sanitizer> | |
163 </param> | |
139 <param name="param_algorithm_pairfinder_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" 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)" help="(-exponent) "/> | 164 <param name="param_algorithm_pairfinder_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" 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)" help="(-exponent) "/> |
140 <param name="param_algorithm_pairfinder_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/> | 165 <param name="param_algorithm_pairfinder_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/> |
141 <param name="param_algorithm_pairfinder_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" 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)" help="(-exponent) "/> | 166 <param name="param_algorithm_pairfinder_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" 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)" help="(-exponent) "/> |
142 <param name="param_algorithm_pairfinder_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/> | 167 <param name="param_algorithm_pairfinder_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/> |
143 <param name="param_algorithm_pairfinder_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/> | 168 <param name="param_algorithm_pairfinder_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/> |
157 <discover_datasets pattern="__designation_and_ext__" directory="results_trafoxml"/> | 182 <discover_datasets pattern="__designation_and_ext__" directory="results_trafoxml"/> |
158 </collection> | 183 </collection> |
159 </outputs> | 184 </outputs> |
160 <help>Corrects retention time distortions between maps using a pose clustering approach. | 185 <help>Corrects retention time distortions between maps using a pose clustering approach. |
161 | 186 |
162 | |
163 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help> | 187 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help> |
164 </tool> | 188 </tool> |