Mercurial > repos > galaxyp > openms_featurelinkerunlabeledkd

comparison FeatureLinkerUnlabeledKD.xml @ 4:17aa0e144300 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:02:25 -0500
parents b73b578a6c11
children c201d5e06f43
comparison
equal deleted inserted replaced
3:b97fe2b25b08 4:17aa0e144300
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 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]--> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <tool id="FeatureLinkerUnlabeledKD" name="FeatureLinkerUnlabeledKD" version="2.2.0"> 4 <tool id="FeatureLinkerUnlabeledKD" name="FeatureLinkerUnlabeledKD" version="2.3.0">
5 <description>Groups corresponding features from multiple maps.</description> 5 <description>Groups corresponding features from multiple maps.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledKD</token> 7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledKD</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
17 $token 17 $token
18 #end for 18 #end for
19 #if $param_out: 19 #if $param_out:
20 -out $param_out 20 -out $param_out
21 #end if 21 #end if
22 #if $param_design:
23 -design $param_design
24 #end if
22 #if $param_keep_subelements: 25 #if $param_keep_subelements:
23 -keep_subelements 26 -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 27 #end if
31 #if $param_algorithm_mz_unit: 28 #if $param_algorithm_mz_unit:
32 -algorithm:mz_unit 29 -algorithm:mz_unit
33 #if " " in str($param_algorithm_mz_unit): 30 #if " " in str($param_algorithm_mz_unit):
34 "$param_algorithm_mz_unit" 31 "$param_algorithm_mz_unit"
35 #else 32 #else
36 $param_algorithm_mz_unit 33 $param_algorithm_mz_unit
37 #end if 34 #end if
38 #end if 35 #end if
39 #if $param_algorithm_warp: 36 #if $param_algorithm_nr_partitions:
40 -algorithm:warp 37 -algorithm:nr_partitions $param_algorithm_nr_partitions
41 #if " " in str($param_algorithm_warp): 38 #end if
42 "$param_algorithm_warp" 39 #if $param_algorithm_warp_enabled:
40 -algorithm:warp:enabled
41 #if " " in str($param_algorithm_warp_enabled):
42 "$param_algorithm_warp_enabled"
43 #else 43 #else
44 $param_algorithm_warp 44 $param_algorithm_warp_enabled
45 #end if 45 #end if
46 #end if 46 #end if
47 #if $param_algorithm_nr_partitions: 47 #if $param_algorithm_warp_rt_tol:
48 -algorithm:nr_partitions $param_algorithm_nr_partitions 48 -algorithm:warp:rt_tol $param_algorithm_warp_rt_tol
49 #end if
50 #if $param_algorithm_warp_mz_tol:
51 -algorithm:warp:mz_tol $param_algorithm_warp_mz_tol
52 #end if
53 #if $param_algorithm_link_rt_tol:
54 -algorithm:link:rt_tol $param_algorithm_link_rt_tol
55 #end if
56 #if $param_algorithm_link_mz_tol:
57 -algorithm:link:mz_tol $param_algorithm_link_mz_tol
49 #end if 58 #end if
50 #if $adv_opts.adv_opts_selector=='advanced': 59 #if $adv_opts.adv_opts_selector=='advanced':
51 #if $adv_opts.param_force: 60 #if $adv_opts.param_force:
52 -force 61 -force
53 #end if 62 #end if
54 #if $adv_opts.param_algorithm_max_pairwise_log_fc: 63 #if $adv_opts.param_algorithm_warp_max_pairwise_log_fc:
55 -algorithm:max_pairwise_log_fc $adv_opts.param_algorithm_max_pairwise_log_fc 64 -algorithm:warp:max_pairwise_log_fc $adv_opts.param_algorithm_warp_max_pairwise_log_fc
56 #end if 65 #end if
57 #if $adv_opts.param_algorithm_min_rel_cc_size: 66 #if $adv_opts.param_algorithm_warp_min_rel_cc_size:
58 -algorithm:min_rel_cc_size $adv_opts.param_algorithm_min_rel_cc_size 67 -algorithm:warp:min_rel_cc_size $adv_opts.param_algorithm_warp_min_rel_cc_size
59 #end if 68 #end if
60 #if $adv_opts.param_algorithm_max_nr_conflicts: 69 #if $adv_opts.param_algorithm_warp_max_nr_conflicts:
61 -algorithm:max_nr_conflicts $adv_opts.param_algorithm_max_nr_conflicts 70 -algorithm:warp:max_nr_conflicts $adv_opts.param_algorithm_warp_max_nr_conflicts
62 #end if 71 #end if
63 #if $adv_opts.param_algorithm_distance_RT_exponent: 72 #if $adv_opts.param_algorithm_distance_RT_exponent:
64 -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent 73 -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
65 #end if 74 #end if
66 #if $adv_opts.param_algorithm_distance_RT_weight: 75 #if $adv_opts.param_algorithm_distance_RT_weight:
120 <remove value="'"/> 129 <remove value="'"/>
121 <remove value="&quot;"/> 130 <remove value="&quot;"/>
122 </valid> 131 </valid>
123 </sanitizer> 132 </sanitizer>
124 </param> 133 </param>
134 <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/>
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) "/> 135 <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) "> 136 <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> 137 <option value="ppm" selected="true">ppm</option>
130 <option value="Da">Da</option> 138 <option value="Da">Da</option>
131 </param> 139 </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) "> 140 <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) "/>
141 <param name="param_algorithm_warp_enabled" 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="(-enabled) ">
133 <option value="true" selected="true">true</option> 142 <option value="true" selected="true">true</option>
134 <option value="false">false</option> 143 <option value="false">false</option>
135 </param> 144 </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) "/> 145 <param name="param_algorithm_warp_rt_tol" type="float" min="0.0" optional="True" value="100.0" label="Width of RT tolerance window (sec)" help="(-rt_tol) "/>
146 <param name="param_algorithm_warp_mz_tol" type="float" min="0.0" optional="True" value="5.0" label="m/z tolerance (in ppm or Da)" help="(-mz_tol) "/>
147 <param name="param_algorithm_link_rt_tol" type="float" min="0.0" optional="True" value="30.0" label="Width of RT tolerance window (sec)" help="(-rt_tol) "/>
148 <param name="param_algorithm_link_mz_tol" type="float" min="0.0" optional="True" value="10.0" label="m/z tolerance (in ppm or Da)" help="(-mz_tol) "/>
137 <expand macro="advanced_options"> 149 <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) "/> 150 <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"/> 151 <param name="param_algorithm_warp_max_pairwise_log_fc" type="float" value="0.5" label="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) "/> 152 <param name="param_algorithm_warp_min_rel_cc_size" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="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) "/> 153 <param name="param_algorithm_warp_max_nr_conflicts" type="integer" min="-1" optional="True" value="0" label="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) "/> 154 <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) "/> 155 <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) "/> 156 <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) "/> 157 <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) "/> 158 <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) "/>