Mercurial > repos > galaxyp > openms_featurelinkerunlabeled

comparison FeatureLinkerUnlabeled.xml @ 0:086cb9f95fef draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:58:28 -0500
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children fad4af2df6a4
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-1:000000000000 0:086cb9f95fef
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="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.1.0">
5 <description>Groups corresponding features from multiple maps.</description>
6 <macros>
7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FeatureLinkerUnlabeled
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_second_nearest_gap:
26 -algorithm:second_nearest_gap $param_algorithm_second_nearest_gap
27 #end if
28 #if $param_algorithm_use_identifications:
29 -algorithm:use_identifications
30 #end if
31 #if $param_algorithm_ignore_charge:
32 -algorithm:ignore_charge
33 #end if
34 #if $param_algorithm_distance_RT_max_difference:
35 -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference
36 #end if
37 #if $param_algorithm_distance_MZ_max_difference:
38 -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference
39 #end if
40 #if $param_algorithm_distance_MZ_unit:
41 -algorithm:distance_MZ:unit $param_algorithm_distance_MZ_unit
42 #end if
43 #if $adv_opts.adv_opts_selector=='advanced':
44 #if $adv_opts.param_force:
45 -force
46 #end if
47 #if $adv_opts.param_algorithm_distance_RT_exponent:
48 -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
49 #end if
50 #if $adv_opts.param_algorithm_distance_RT_weight:
51 -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
52 #end if
53 #if $adv_opts.param_algorithm_distance_MZ_exponent:
54 -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
55 #end if
56 #if $adv_opts.param_algorithm_distance_MZ_weight:
57 -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
58 #end if
59 #if $adv_opts.param_algorithm_distance_intensity_exponent:
60 -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
61 #end if
62 #if $adv_opts.param_algorithm_distance_intensity_weight:
63 -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
64 #end if
65 #end if
66 </command>
67 <inputs>
68 <param name="param_in" type="data" format="featurexml,consensusxml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) ">
69 <sanitizer>
70 <valid initial="string.printable">
71 <remove value="'"/>
72 <remove value="&quot;"/>
73 </valid>
74 </sanitizer>
75 </param>
76 <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) "/>
77 <param name="param_algorithm_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" 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" help="(-second_nearest_gap) "/>
78 <param name="param_algorithm_use_identifications" display="radio" type="boolean" truevalue="-algorithm:use_identifications" falsevalue="" checked="false" optional="True" 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)" help="(-use_identifications) "/>
79 <param name="param_algorithm_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/>
80 <param name="param_algorithm_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/>
81 <param name="param_algorithm_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/>
82 <param name="param_algorithm_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) ">
83 <option value="Da" selected="true">Da</option>
84 <option value="ppm">ppm</option>
85 </param>
86 <expand macro="advanced_options">
87 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
88 <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) "/>
89 <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) "/>
90 <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) "/>
91 <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) "/>
92 <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) "/>
93 <param name="param_algorithm_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/>
94 </expand>
95 </inputs>
96 <outputs>
97 <data name="param_out" format="consensusxml"/>
98 </outputs>
99 <help>Groups corresponding features from multiple maps.
100
101
102 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html</help>
103 </tool>