comparison FeatureLinkerLabeled.xml @ 0:2fe5ef9f1760 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:45:07 -0500
parents
children 77f29f5244d9
comparison
equal deleted inserted replaced
-1:000000000000 0:2fe5ef9f1760
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="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="2.1.0">
5 <description>Groups corresponding isotope-labeled features in a feature map.</description>
6 <macros>
7 <token name="@EXECUTABLE@">FeatureLinkerLabeled</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FeatureLinkerLabeled
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_algorithm_rt_estimate:
22 -algorithm:rt_estimate $param_algorithm_rt_estimate
23 #end if
24 #if $param_algorithm_rt_pair_dist:
25 -algorithm:rt_pair_dist $param_algorithm_rt_pair_dist
26 #end if
27 #if $param_algorithm_rt_dev_low:
28 -algorithm:rt_dev_low $param_algorithm_rt_dev_low
29 #end if
30 #if $param_algorithm_rt_dev_high:
31 -algorithm:rt_dev_high $param_algorithm_rt_dev_high
32 #end if
33
34 #if $rep_param_algorithm_mz_pair_dists:
35 -algorithm:mz_pair_dists
36 #for token in $rep_param_algorithm_mz_pair_dists:
37 #if " " in str(token):
38 "$token.param_algorithm_mz_pair_dists"
39 #else
40 $token.param_algorithm_mz_pair_dists
41 #end if
42 #end for
43 #end if
44 #if $param_algorithm_mz_dev:
45 -algorithm:mz_dev $param_algorithm_mz_dev
46 #end if
47 #if $adv_opts.adv_opts_selector=='advanced':
48 #if $adv_opts.param_force:
49 -force
50 #end if
51 #if $adv_opts.param_algorithm_mrm:
52 -algorithm:mrm
53 #end if
54 #end if
55 </command>
56 <inputs>
57 <param name="param_in" type="data" format="featurexml" optional="False" label="Input file" help="(-in) "/>
58 <param name="param_algorithm_rt_estimate" display="radio" type="select" optional="False" value="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">
59 <option value="true" selected="true">true</option>
60 <option value="false">false</option>
61 </param>
62 <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) "/>
63 <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) "/>
64 <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) "/>
65 <repeat name="rep_param_algorithm_mz_pair_dists" min="0" max="1" title="param_algorithm_mz_pair_dists">
66 <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)">
67 <sanitizer>
68 <valid initial="string.printable">
69 <remove value="'"/>
70 <remove value="&quot;"/>
71 </valid>
72 </sanitizer>
73 </param>
74 </repeat>
75 <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) "/>
76 <expand macro="advanced_options">
77 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
78 <param name="param_algorithm_mrm" display="radio" 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) "/>
79 </expand>
80 </inputs>
81 <outputs>
82 <data name="param_out" format="consensusxml"/>
83 </outputs>
84 <help>Groups corresponding isotope-labeled features in a feature map.
85
86
87 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html</help>
88 </tool>