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comparison FeatureLinkerUnlabeled.xml @ 4:6ead64a594bd draft default tip

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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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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="1.12.0"> 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 <description>Groups corresponding features from multiple maps.</description> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <macros> 4 <tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.0.0">
5 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token> 5 <description>Groups corresponding features from multiple maps.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>FeatureLinkerUnlabeled 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FeatureLinkerUnlabeled
11 14
12 -in ${param_in} 15 -in
13 -out ${param_out} 16 #for token in $param_in:
14 ${param_keep_subelements} 17 $token
15 -threads \${GALAXY_SLOTS:-24} 18 #end for
16 -algorithm:second_nearest_gap ${param_second_nearest_gap} 19 #if $param_out:
17 ${param_use_identifications} 20 -out $param_out
18 ${param_ignore_charge} 21 #end if
19 -algorithm:distance_RT:max_difference ${param_max_difference} 22 #if $param_keep_subelements:
20 -algorithm:distance_MZ:max_difference ${param_max_difference} 23 -keep_subelements
21 -algorithm:distance_MZ:unit ${param_unit} 24 #end if
25 -threads \${GALAXY_SLOTS:-24}
26 #if $param_algorithm_second_nearest_gap:
27 -algorithm:second_nearest_gap $param_algorithm_second_nearest_gap
28 #end if
29 #if $param_algorithm_use_identifications:
30 -algorithm:use_identifications
31 #end if
32 #if $param_algorithm_ignore_charge:
33 -algorithm:ignore_charge
34 #end if
35 #if $param_algorithm_distance_RT_max_difference:
36 -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference
37 #end if
38 #if $param_algorithm_distance_MZ_max_difference:
39 -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference
40 #end if
41 #if $param_algorithm_distance_MZ_unit:
42 -algorithm:distance_MZ:unit
43 #if &quot; &quot; in str($param_algorithm_distance_MZ_unit):
44 &quot;$param_algorithm_distance_MZ_unit&quot;
45 #else
46 $param_algorithm_distance_MZ_unit
47 #end if
48 #end if
22 #if $adv_opts.adv_opts_selector=='advanced': 49 #if $adv_opts.adv_opts_selector=='advanced':
23 -algorithm:distance_RT:exponent ${adv_opts.param_exponent} 50 #if $adv_opts.param_force:
24 -algorithm:distance_RT:weight ${adv_opts.param_weight} 51 -force
25 -algorithm:distance_MZ:exponent ${adv_opts.param_exponent} 52 #end if
26 -algorithm:distance_MZ:weight ${adv_opts.param_weight} 53 #if $adv_opts.param_algorithm_distance_RT_exponent:
27 -algorithm:distance_intensity:exponent ${adv_opts.param_exponent} 54 -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
28 -algorithm:distance_intensity:weight ${adv_opts.param_weight} 55 #end if
56 #if $adv_opts.param_algorithm_distance_RT_weight:
57 -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
58 #end if
59 #if $adv_opts.param_algorithm_distance_MZ_exponent:
60 -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
61 #end if
62 #if $adv_opts.param_algorithm_distance_MZ_weight:
63 -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
64 #end if
65 #if $adv_opts.param_algorithm_distance_intensity_exponent:
66 -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
67 #end if
68 #if $adv_opts.param_algorithm_distance_intensity_weight:
69 -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
70 #end if
29 #end if 71 #end if
30 </command> 72 </command>
31 <inputs> 73 <inputs>
32 <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" size="20" label="input files separated by blanks" help="(-in)"/> 74 <param format="xml,consensusxml" help="(-in) " label="input files separated by blanks" multiple="true" name="param_in" optional="False" size="30" type="data">
33 <param name="param_keep_subelements" type="boolean" truevalue="-keep_subelements true" falsevalue="-keep_subelements false" 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)"/> 75 <sanitizer>
34 <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)"/> 76 <valid initial="string.printable">
35 <param name="param_use_identifications" type="boolean" truevalue="-algorithm:use_identifications true" falsevalue="-algorithm: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)"/> 77 <remove value="'"/>
36 <param name="param_ignore_charge" type="boolean" truevalue="-algorithm:ignore_charge true" falsevalue="-algorithm:ignore_charge false" checked="false" optional="True" label="Compare features normally even if their charge states are different" help="(-ignore_charge)"/> 78 <remove value="&quot;"/>
37 <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)"/> 79 </valid>
38 <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)"/> 80 </sanitizer>
39 <param name="param_unit" type="select" optional="True" value="Da" label="Unit of the 'max_difference' parameter" help="(-unit)"> 81 </param>
40 <option value="Da">Da</option> 82 <param checked="false" falsevalue="" help="(-keep_subelements) " label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" name="param_keep_subelements" optional="True" truevalue="-keep_subelements" type="boolean"/>
41 <option value="ppm">ppm</option> 83 <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_second_nearest_gap" optional="True" type="float" value="2.0"/>
42 </param> 84 <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_use_identifications" optional="True" truevalue="-algorithm:use_identifications" type="boolean"/>
43 <expand macro="advanced_options"> 85 <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_ignore_charge" optional="True" truevalue="-algorithm:ignore_charge" type="boolean"/>
44 <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)"/> 86 <param help="(-max_difference) " label="Never pair features with a larger RT distance (in seconds)" min="0.0" name="param_algorithm_distance_RT_max_difference" optional="True" type="float" value="100.0"/>
45 <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="RT distances are weighted by this factor" help="(-weight)"/> 87 <param help="(-max_difference) " label="Never pair features with larger m/z distance (unit defined by 'unit')" min="0.0" name="param_algorithm_distance_MZ_max_difference" optional="True" type="float" value="0.3"/>
46 <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)"/> 88 <param help="(-unit) " label="Unit of the 'max_difference' paramete" name="param_algorithm_distance_MZ_unit" optional="True" type="select" value="Da">
47 <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)"/> 89 <option value="Da">Da</option>
48 <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)"/> 90 <option value="ppm">ppm</option>
49 <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)"/> 91 </param>
50 </expand> 92 <expand macro="advanced_options">
51 </inputs> 93 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
52 <outputs> 94 <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_distance_RT_exponent" optional="True" type="float" value="1.0"/>
53 <data name="param_out" label="Output file" format="consensusXML"/> 95 <param help="(-weight) " label="Final RT distances are weighted by this facto" min="0.0" name="param_algorithm_distance_RT_weight" optional="True" type="float" value="1.0"/>
54 </outputs> 96 <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_distance_MZ_exponent" optional="True" type="float" value="2.0"/>
55 <help>**What it does** 97 <param help="(-weight) " label="Final m/z distances are weighted by this facto" min="0.0" name="param_algorithm_distance_MZ_weight" optional="True" type="float" value="1.0"/>
56 98 <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_distance_intensity_exponent" optional="True" type="float" value="1.0"/>
57 Groups corresponding features from multiple maps. 99 <param help="(-weight) " label="Final intensity distances are weighted by this facto" min="0.0" name="param_algorithm_distance_intensity_weight" optional="True" type="float" value="0.0"/>
100 </expand>
101 </inputs>
102 <outputs>
103 <data format="consensusxml" name="param_out"/>
104 </outputs>
105 <help>Groups corresponding features from multiple maps.
58 106
59 107
60 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html 108 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html</help>
61 109 </tool>
62 @REFERENCES@
63 </help>
64 </tool>