|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="2.0.0">
|
|
|
3 <description>Groups corresponding isotope-labeled features in a feature map.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">FeatureLinkerLabeled</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>FeatureLinkerLabeled
|
|
|
11
|
|
|
12 #if $param_in:
|
|
|
13 -in $param_in
|
|
|
14 #end if
|
|
|
15 #if $param_out:
|
|
|
16 -out $param_out
|
|
|
17 #end if
|
|
|
18 -threads \${GALAXY_SLOTS:-24}
|
|
|
19 #if $param_algorithm_rt_estimate:
|
|
|
20 -algorithm:rt_estimate
|
|
|
21 #end if
|
|
|
22 #if $param_algorithm_rt_pair_dist:
|
|
|
23 -algorithm:rt_pair_dist $param_algorithm_rt_pair_dist
|
|
|
24 #end if
|
|
|
25 #if $param_algorithm_rt_dev_low:
|
|
|
26 -algorithm:rt_dev_low $param_algorithm_rt_dev_low
|
|
|
27 #end if
|
|
|
28 #if $param_algorithm_rt_dev_high:
|
|
|
29 -algorithm:rt_dev_high $param_algorithm_rt_dev_high
|
|
|
30 #end if
|
|
|
31
|
|
|
32 #if $rep_param_algorithm_mz_pair_dists:
|
|
|
33 -algorithm:mz_pair_dists
|
|
|
34 #for token in $rep_param_algorithm_mz_pair_dists:
|
|
|
35 #if " " in str(token):
|
|
|
36 "$token.param_algorithm_mz_pair_dists"
|
|
|
37 #else
|
|
|
38 $token.param_algorithm_mz_pair_dists
|
|
|
39 #end if
|
|
|
40 #end for
|
|
|
41 #end if
|
|
|
42 #if $param_algorithm_mz_dev:
|
|
|
43 -algorithm:mz_dev $param_algorithm_mz_dev
|
|
|
44 #end if
|
|
|
45 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
46 #if $adv_opts.param_force:
|
|
|
47 -force
|
|
|
48 #end if
|
|
|
49 #if $adv_opts.param_algorithm_mrm:
|
|
|
50 -algorithm:mrm
|
|
|
51 #end if
|
|
|
52 #end if
|
|
|
53 </command>
|
|
|
54 <inputs>
|
|
|
55 <param name="param_in" type="data" format="featurexml" optional="False" label="Input file" help="(-in) "/>
|
|
|
56 <param name="param_algorithm_rt_estimate" type="boolean" truevalue="-algorithm:rt_estimate" falsevalue="" checked="true" optional="True" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" help="(-rt_estimate) Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance"/>
|
|
|
57 <param name="param_algorithm_rt_pair_dist" type="float" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help="(-rt_pair_dist) "/>
|
|
|
58 <param name="param_algorithm_rt_dev_low" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation below optimal retention time distance" help="(-rt_dev_low) "/>
|
|
|
59 <param name="param_algorithm_rt_dev_high" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation above optimal retention time distance" help="(-rt_dev_high) "/>
|
|
|
60 <repeat name="rep_param_algorithm_mz_pair_dists" min="0" max="1" title="param_algorithm_mz_pair_dists">
|
|
|
61 <param name="param_algorithm_mz_pair_dists" type="text" size="30" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, ." help="(-mz_pair_dists) by division through charge)">
|
|
|
62 <sanitizer>
|
|
|
63 <valid initial="string.printable">
|
|
|
64 <remove value="'"/>
|
|
|
65 <remove value="""/>
|
|
|
66 </valid>
|
|
|
67 </sanitizer>
|
|
|
68 </param>
|
|
|
69 </repeat>
|
|
|
70 <param name="param_algorithm_mz_dev" type="float" min="0.0" optional="True" value="0.05" label="maximum allowed deviation from optimal m/z distance" help="(-mz_dev) "/>
|
|
|
71 <expand macro="advanced_options">
|
|
|
72 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
73 <param name="param_algorithm_mrm" type="boolean" truevalue="-algorithm:mrm" falsevalue="" checked="false" optional="True" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help="(-mrm) "/>
|
|
|
74 </expand>
|
|
|
75 </inputs>
|
|
|
76 <outputs>
|
|
|
77 <data name="param_out" format="consensusxml"/>
|
|
|
78 </outputs>
|
|
|
79 <help>**What it does**
|
|
|
80
|
|
|
81 Groups corresponding isotope-labeled features in a feature map.
|
|
|
82
|
|
|
83
|
|
|
84 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html</help>
|
|
|
85 <expand macro="references"/>
|
|
|
86 </tool>
|
