|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.0.0">
|
|
|
3 <description>Groups corresponding features from multiple maps.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>FeatureLinkerUnlabeled
|
|
|
11
|
|
|
12 -in
|
|
|
13 #for token in $param_in:
|
|
|
14 $token
|
|
|
15 #end for
|
|
|
16 #if $param_out:
|
|
|
17 -out $param_out
|
|
|
18 #end if
|
|
|
19 #if $param_keep_subelements:
|
|
|
20 -keep_subelements
|
|
|
21 #end if
|
|
|
22 -threads \${GALAXY_SLOTS:-24}
|
|
|
23 #if $param_algorithm_second_nearest_gap:
|
|
|
24 -algorithm:second_nearest_gap $param_algorithm_second_nearest_gap
|
|
|
25 #end if
|
|
|
26 #if $param_algorithm_use_identifications:
|
|
|
27 -algorithm:use_identifications
|
|
|
28 #end if
|
|
|
29 #if $param_algorithm_ignore_charge:
|
|
|
30 -algorithm:ignore_charge
|
|
|
31 #end if
|
|
|
32 #if $param_algorithm_distance_RT_max_difference:
|
|
|
33 -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference
|
|
|
34 #end if
|
|
|
35 #if $param_algorithm_distance_MZ_max_difference:
|
|
|
36 -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference
|
|
|
37 #end if
|
|
|
38 #if $param_algorithm_distance_MZ_unit:
|
|
|
39 -algorithm:distance_MZ:unit
|
|
|
40 #if " " in str($param_algorithm_distance_MZ_unit):
|
|
|
41 "$param_algorithm_distance_MZ_unit"
|
|
|
42 #else
|
|
|
43 $param_algorithm_distance_MZ_unit
|
|
|
44 #end if
|
|
|
45 #end if
|
|
|
46 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
47 #if $adv_opts.param_force:
|
|
|
48 -force
|
|
|
49 #end if
|
|
|
50 #if $adv_opts.param_algorithm_distance_RT_exponent:
|
|
|
51 -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
|
|
|
52 #end if
|
|
|
53 #if $adv_opts.param_algorithm_distance_RT_weight:
|
|
|
54 -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
|
|
|
55 #end if
|
|
|
56 #if $adv_opts.param_algorithm_distance_MZ_exponent:
|
|
|
57 -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
|
|
|
58 #end if
|
|
|
59 #if $adv_opts.param_algorithm_distance_MZ_weight:
|
|
|
60 -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
|
|
|
61 #end if
|
|
|
62 #if $adv_opts.param_algorithm_distance_intensity_exponent:
|
|
|
63 -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
|
|
|
64 #end if
|
|
|
65 #if $adv_opts.param_algorithm_distance_intensity_weight:
|
|
|
66 -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
|
|
|
67 #end if
|
|
|
68 #end if
|
|
|
69 </command>
|
|
|
70 <inputs>
|
|
|
71 <param name="param_in" type="data" format="featurexml,consensusxml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) ">
|
|
|
72 <sanitizer>
|
|
|
73 <valid initial="string.printable">
|
|
|
74 <remove value="'"/>
|
|
|
75 <remove value="""/>
|
|
|
76 </valid>
|
|
|
77 </sanitizer>
|
|
|
78 </param>
|
|
|
79 <param name="param_keep_subelements" 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) "/>
|
|
|
80 <param name="param_algorithm_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) "/>
|
|
|
81 <param name="param_algorithm_use_identifications" type="boolean" truevalue="-algorithm:use_identifications" falsevalue="" 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) "/>
|
|
|
82 <param name="param_algorithm_ignore_charge" type="boolean" truevalue="-algorithm:ignore_charge" falsevalue="" checked="false" optional="True" label="Compare features normally even if their charge states are different" help="(-ignore_charge) "/>
|
|
|
83 <param name="param_algorithm_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Maximum allowed difference in RT in seconds" help="(-max_difference) "/>
|
|
|
84 <param name="param_algorithm_distance_MZ_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) "/>
|
|
|
85 <param name="param_algorithm_distance_MZ_unit" type="select" optional="True" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) ">
|
|
|
86 <option value="Da">Da</option>
|
|
|
87 <option value="ppm">ppm</option>
|
|
|
88 </param>
|
|
|
89 <expand macro="advanced_options">
|
|
|
90 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
91 <param name="param_algorithm_distance_RT_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) "/>
|
|
|
92 <param name="param_algorithm_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="RT distances are weighted by this facto" help="(-weight) "/>
|
|
|
93 <param name="param_algorithm_distance_MZ_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) "/>
|
|
|
94 <param name="param_algorithm_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="m/z distances are weighted by this facto" help="(-weight) "/>
|
|
|
95 <param name="param_algorithm_distance_intensity_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) "/>
|
|
|
96 <param name="param_algorithm_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Distances based on relative intensity are weighted by this facto" help="(-weight) "/>
|
|
|
97 </expand>
|
|
|
98 </inputs>
|
|
|
99 <outputs>
|
|
|
100 <data name="param_out" format="consensusxml"/>
|
|
|
101 </outputs>
|
|
|
102 <help>**What it does**
|
|
|
103
|
|
|
104 Groups corresponding features from multiple maps.
|
|
|
105
|
|
|
106
|
|
|
107 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html</help>
|
|
|
108 <expand macro="references"/>
|
|
|
109 </tool>
|
