Mercurial > repos > galaxyp > openms_featurelinkerunlabeledkd

comparison FeatureLinkerUnlabeledKD.xml @ 0:b73b578a6c11 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:34:25 -0400
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children 17aa0e144300
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-1:000000000000 0:b73b578a6c11
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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Map Alignment]-->
4 <tool id="FeatureLinkerUnlabeledKD" name="FeatureLinkerUnlabeledKD" version="2.2.0">
5 <description>Groups corresponding features from multiple maps.</description>
6 <macros>
7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledKD</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FeatureLinkerUnlabeledKD
14
15 -in
16 #for token in $param_in:
17 $token
18 #end for
19 #if $param_out:
20 -out $param_out
21 #end if
22 #if $param_keep_subelements:
23 -keep_subelements
24 #end if
25 #if $param_algorithm_rt_tol:
26 -algorithm:rt_tol $param_algorithm_rt_tol
27 #end if
28 #if $param_algorithm_mz_tol:
29 -algorithm:mz_tol $param_algorithm_mz_tol
30 #end if
31 #if $param_algorithm_mz_unit:
32 -algorithm:mz_unit
33 #if " " in str($param_algorithm_mz_unit):
34 "$param_algorithm_mz_unit"
35 #else
36 $param_algorithm_mz_unit
37 #end if
38 #end if
39 #if $param_algorithm_warp:
40 -algorithm:warp
41 #if " " in str($param_algorithm_warp):
42 "$param_algorithm_warp"
43 #else
44 $param_algorithm_warp
45 #end if
46 #end if
47 #if $param_algorithm_nr_partitions:
48 -algorithm:nr_partitions $param_algorithm_nr_partitions
49 #end if
50 #if $adv_opts.adv_opts_selector=='advanced':
51 #if $adv_opts.param_force:
52 -force
53 #end if
54 #if $adv_opts.param_algorithm_max_pairwise_log_fc:
55 -algorithm:max_pairwise_log_fc $adv_opts.param_algorithm_max_pairwise_log_fc
56 #end if
57 #if $adv_opts.param_algorithm_min_rel_cc_size:
58 -algorithm:min_rel_cc_size $adv_opts.param_algorithm_min_rel_cc_size
59 #end if
60 #if $adv_opts.param_algorithm_max_nr_conflicts:
61 -algorithm:max_nr_conflicts $adv_opts.param_algorithm_max_nr_conflicts
62 #end if
63 #if $adv_opts.param_algorithm_distance_RT_exponent:
64 -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
65 #end if
66 #if $adv_opts.param_algorithm_distance_RT_weight:
67 -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
68 #end if
69 #if $adv_opts.param_algorithm_distance_MZ_exponent:
70 -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
71 #end if
72 #if $adv_opts.param_algorithm_distance_MZ_weight:
73 -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
74 #end if
75 #if $adv_opts.param_algorithm_distance_intensity_exponent:
76 -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
77 #end if
78 #if $adv_opts.param_algorithm_distance_intensity_weight:
79 -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
80 #end if
81 #if $adv_opts.param_algorithm_distance_intensity_log_transform:
82 -algorithm:distance_intensity:log_transform
83 #if " " in str($adv_opts.param_algorithm_distance_intensity_log_transform):
84 "$adv_opts.param_algorithm_distance_intensity_log_transform"
85 #else
86 $adv_opts.param_algorithm_distance_intensity_log_transform
87 #end if
88 #end if
89 #if $adv_opts.param_algorithm_LOWESS_span:
90 -algorithm:LOWESS:span $adv_opts.param_algorithm_LOWESS_span
91 #end if
92 #if $adv_opts.param_algorithm_LOWESS_num_iterations:
93 -algorithm:LOWESS:num_iterations $adv_opts.param_algorithm_LOWESS_num_iterations
94 #end if
95 #if $adv_opts.param_algorithm_LOWESS_delta:
96 -algorithm:LOWESS:delta $adv_opts.param_algorithm_LOWESS_delta
97 #end if
98 #if $adv_opts.param_algorithm_LOWESS_interpolation_type:
99 -algorithm:LOWESS:interpolation_type
100 #if " " in str($adv_opts.param_algorithm_LOWESS_interpolation_type):
101 "$adv_opts.param_algorithm_LOWESS_interpolation_type"
102 #else
103 $adv_opts.param_algorithm_LOWESS_interpolation_type
104 #end if
105 #end if
106 #if $adv_opts.param_algorithm_LOWESS_extrapolation_type:
107 -algorithm:LOWESS:extrapolation_type
108 #if " " in str($adv_opts.param_algorithm_LOWESS_extrapolation_type):
109 "$adv_opts.param_algorithm_LOWESS_extrapolation_type"
110 #else
111 $adv_opts.param_algorithm_LOWESS_extrapolation_type
112 #end if
113 #end if
114 #end if
115 </command>
116 <inputs>
117 <param name="param_in" type="data" format="featurexml,consensusxml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) ">
118 <sanitizer>
119 <valid initial="string.printable">
120 <remove value="'"/>
121 <remove value="&quot;"/>
122 </valid>
123 </sanitizer>
124 </param>
125 <param name="param_keep_subelements" display="radio" type="boolean" truevalue="-keep_subelements" falsevalue="" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help="(-keep_subelements) "/>
126 <param name="param_algorithm_rt_tol" type="float" min="0.0" optional="True" value="60.0" label="Width of RT tolerance window (sec)" help="(-rt_tol) "/>
127 <param name="param_algorithm_mz_tol" type="float" min="0.0" optional="True" value="15.0" label="m/z tolerance (in ppm or Da)" help="(-mz_tol) "/>
128 <param name="param_algorithm_mz_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of m/z tolerance" help="(-mz_unit) ">
129 <option value="ppm" selected="true">ppm</option>
130 <option value="Da">Da</option>
131 </param>
132 <param name="param_algorithm_warp" display="radio" type="select" optional="False" value="true" label="Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)" help="(-warp) ">
133 <option value="true" selected="true">true</option>
134 <option value="false">false</option>
135 </param>
136 <param name="param_algorithm_nr_partitions" type="integer" min="1" optional="True" value="100" label="Number of partitions in m/z space" help="(-nr_partitions) "/>
137 <expand macro="advanced_options">
138 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
139 <param name="param_algorithm_max_pairwise_log_fc" type="float" value="0.5" label="Only relevant during RT alignment ('warp' set to 'true'): Maximum absolute log10 fold change between two compatible signals during compatibility graph construction" help="(-max_pairwise_log_fc) Two signals from different maps will not be connected by an edge in the compatibility graph if absolute log fold change exceeds this limit (they might still end up in the same connected component, however). Note: this does not limit fold changes in the linking stage, only during RT alignment, where we try to find high-quality alignment anchor points. Setting this to a value &lt; 0 disables the FC check"/>
140 <param name="param_algorithm_min_rel_cc_size" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Only relevant during RT alignment ('warp' set to 'true'): Only connected components containing compatible features from at least max(2, (warp_min_occur * number_of_input_maps)) input maps are considered for computing the warping function" help="(-min_rel_cc_size) "/>
141 <param name="param_algorithm_max_nr_conflicts" type="integer" min="-1" optional="True" value="0" label="Only relevant during RT alignment ('warp' set to 'true'): Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)" help="(-max_nr_conflicts) "/>
142 <param name="param_algorithm_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) "/>
143 <param name="param_algorithm_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/>
144 <param name="param_algorithm_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) "/>
145 <param name="param_algorithm_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) "/>
146 <param name="param_algorithm_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) "/>
147 <param name="param_algorithm_distance_intensity_weight" type="float" min="0.0" optional="True" value="1.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/>
148 <param name="param_algorithm_distance_intensity_log_transform" display="radio" type="select" optional="False" value="enabled" label="Log-transform intensities?" help="(-log_transform) If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
149 <option value="enabled" selected="true">enabled</option>
150 <option value="disabled">disabled</option>
151 </param>
152 <param name="param_algorithm_LOWESS_span" type="float" min="0.0" max="1.0" optional="True" value="0.666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="(-span) Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
153 <param name="param_algorithm_LOWESS_num_iterations" type="integer" min="0" optional="True" value="3" label="Number of robustifying iterations for lowess fitting" help="(-num_iterations) "/>
154 <param name="param_algorithm_LOWESS_delta" type="float" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input," help="(-delta) e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
155 <param name="param_algorithm_LOWESS_interpolation_type" display="radio" type="select" optional="False" value="cspline" label="Method to use for interpolation between datapoints computed by lowess" help="(-interpolation_type) 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
156 <option value="linear">linear</option>
157 <option value="cspline" selected="true">cspline</option>
158 <option value="akima">akima</option>
159 </param>
160 <param name="param_algorithm_LOWESS_extrapolation_type" display="radio" type="select" optional="False" value="four-point-linear" label="Method to use for extrapolation outside the data range" help="(-extrapolation_type) 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
161 <option value="two-point-linear">two-point-linear</option>
162 <option value="four-point-linear" selected="true">four-point-linear</option>
163 <option value="global-linear">global-linear</option>
164 </param>
165 </expand>
166 </inputs>
167 <outputs>
168 <data name="param_out" format="consensusxml"/>
169 </outputs>
170 <help>Groups corresponding features from multiple maps.
171
172
173 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeledKD.html</help>
174 </tool>