Mercurial > repos > galaxyp > openms_metaboliteadductdecharger

comparison MetaboliteAdductDecharger.xml @ 0:ca7fce38ea1f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:06:22 -0500
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children d37e3dc967b9
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-1:000000000000 0:ca7fce38ea1f
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 CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MetaboliteAdductDecharger" name="MetaboliteAdductDecharger" version="2.3.0">
5 <description>Decharges and merges different feature charge variants of the same metabolite.</description>
6 <macros>
7 <token name="@EXECUTABLE@">MetaboliteAdductDecharger</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MetaboliteAdductDecharger
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out_cm:
19 -out_cm $param_out_cm
20 #end if
21 #if $param_out_fm:
22 -out_fm $param_out_fm
23 #end if
24 #if $param_outpairs:
25 -outpairs $param_outpairs
26 #end if
27 #if $param_algorithm_MetaboliteFeatureDeconvolution_charge_min:
28 -algorithm:MetaboliteFeatureDeconvolution:charge_min $param_algorithm_MetaboliteFeatureDeconvolution_charge_min
29 #end if
30 #if $param_algorithm_MetaboliteFeatureDeconvolution_charge_max:
31 -algorithm:MetaboliteFeatureDeconvolution:charge_max $param_algorithm_MetaboliteFeatureDeconvolution_charge_max
32 #end if
33 #if $param_algorithm_MetaboliteFeatureDeconvolution_charge_span_max:
34 -algorithm:MetaboliteFeatureDeconvolution:charge_span_max $param_algorithm_MetaboliteFeatureDeconvolution_charge_span_max
35 #end if
36 #if $param_algorithm_MetaboliteFeatureDeconvolution_q_try:
37 -algorithm:MetaboliteFeatureDeconvolution:q_try
38 #if " " in str($param_algorithm_MetaboliteFeatureDeconvolution_q_try):
39 "$param_algorithm_MetaboliteFeatureDeconvolution_q_try"
40 #else
41 $param_algorithm_MetaboliteFeatureDeconvolution_q_try
42 #end if
43 #end if
44 #if $param_algorithm_MetaboliteFeatureDeconvolution_retention_max_diff:
45 -algorithm:MetaboliteFeatureDeconvolution:retention_max_diff $param_algorithm_MetaboliteFeatureDeconvolution_retention_max_diff
46 #end if
47 #if $param_algorithm_MetaboliteFeatureDeconvolution_retention_max_diff_local:
48 -algorithm:MetaboliteFeatureDeconvolution:retention_max_diff_local $param_algorithm_MetaboliteFeatureDeconvolution_retention_max_diff_local
49 #end if
50 #if $param_algorithm_MetaboliteFeatureDeconvolution_mass_max_diff:
51 -algorithm:MetaboliteFeatureDeconvolution:mass_max_diff $param_algorithm_MetaboliteFeatureDeconvolution_mass_max_diff
52 #end if
53
54 #if $rep_param_algorithm_MetaboliteFeatureDeconvolution_potential_adducts:
55 -algorithm:MetaboliteFeatureDeconvolution:potential_adducts
56 #for token in $rep_param_algorithm_MetaboliteFeatureDeconvolution_potential_adducts:
57 #if " " in str(token):
58 "$token.param_algorithm_MetaboliteFeatureDeconvolution_potential_adducts"
59 #else
60 $token.param_algorithm_MetaboliteFeatureDeconvolution_potential_adducts
61 #end if
62 #end for
63 #end if
64 #if $param_algorithm_MetaboliteFeatureDeconvolution_max_neutrals:
65 -algorithm:MetaboliteFeatureDeconvolution:max_neutrals $param_algorithm_MetaboliteFeatureDeconvolution_max_neutrals
66 #end if
67 #if $param_algorithm_MetaboliteFeatureDeconvolution_max_minority_bound:
68 -algorithm:MetaboliteFeatureDeconvolution:max_minority_bound $param_algorithm_MetaboliteFeatureDeconvolution_max_minority_bound
69 #end if
70 #if $param_algorithm_MetaboliteFeatureDeconvolution_min_rt_overlap:
71 -algorithm:MetaboliteFeatureDeconvolution:min_rt_overlap $param_algorithm_MetaboliteFeatureDeconvolution_min_rt_overlap
72 #end if
73 #if $param_algorithm_MetaboliteFeatureDeconvolution_intensity_filter:
74 -algorithm:MetaboliteFeatureDeconvolution:intensity_filter
75 #end if
76 #if $param_algorithm_MetaboliteFeatureDeconvolution_negative_mode:
77 -algorithm:MetaboliteFeatureDeconvolution:negative_mode "$param_algorithm_MetaboliteFeatureDeconvolution_negative_mode"
78 #end if
79 #if $adv_opts.adv_opts_selector=='advanced':
80 #if $adv_opts.param_force:
81 -force
82 #end if
83 #if $adv_opts.param_algorithm_MetaboliteFeatureDeconvolution_default_map_label:
84 -algorithm:MetaboliteFeatureDeconvolution:default_map_label "$adv_opts.param_algorithm_MetaboliteFeatureDeconvolution_default_map_label"
85 #end if
86 #if $adv_opts.param_algorithm_MetaboliteFeatureDeconvolution_verbose_level:
87 -algorithm:MetaboliteFeatureDeconvolution:verbose_level $adv_opts.param_algorithm_MetaboliteFeatureDeconvolution_verbose_level
88 #end if
89 #end if
90 </command>
91 <inputs>
92 <param name="param_in" type="data" format="featurexml" optional="False" label="input file" help="(-in) "/>
93 <param name="param_algorithm_MetaboliteFeatureDeconvolution_charge_min" type="integer" value="1" label="Minimal possible charge" help="(-charge_min) "/>
94 <param name="param_algorithm_MetaboliteFeatureDeconvolution_charge_max" type="integer" value="3" label="Maximal possible charge" help="(-charge_max) "/>
95 <param name="param_algorithm_MetaboliteFeatureDeconvolution_charge_span_max" type="integer" min="1" optional="True" value="3" label="Maximal range of charges for a single analyte, i.e" help="(-charge_span_max) observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge"/>
96 <param name="param_algorithm_MetaboliteFeatureDeconvolution_q_try" display="radio" type="select" optional="False" value="feature" label="Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature')" help="(-q_try) ">
97 <option value="feature" selected="true">feature</option>
98 <option value="heuristic">heuristic</option>
99 <option value="all">all</option>
100 </param>
101 <param name="param_algorithm_MetaboliteFeatureDeconvolution_retention_max_diff" type="float" value="1.0" label="Maximum allowed RT difference between any two features if their relation shall be determined" help="(-retention_max_diff) "/>
102 <param name="param_algorithm_MetaboliteFeatureDeconvolution_retention_max_diff_local" type="float" value="1.0" label="Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)" help="(-retention_max_diff_local) "/>
103 <param name="param_algorithm_MetaboliteFeatureDeconvolution_mass_max_diff" type="float" value="0.05" label="Maximum allowed mass difference [in Th] for a single feature" help="(-mass_max_diff) "/>
104 <repeat name="rep_param_algorithm_MetaboliteFeatureDeconvolution_potential_adducts" min="0" max="1" title="param_algorithm_MetaboliteFeatureDeconvolution_potential_adducts">
105 <param name="param_algorithm_MetaboliteFeatureDeconvolution_potential_adducts" type="text" size="30" value="K:+:0.1" label="Adducts used to explain mass differences in format: 'Element:Charge(+/-):Probability[:RTShift[:Label]]', i.e. the number of '+' or '-' indicate the charge," help="(-potential_adducts) e.g. 'Ca:++:0.5' indicates +2. Probabilites have to be in (0,1]. RTShift param is optional and indicates the expected RT shift caused by this adduct, e.g. '(2)H4H-4:0:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As a fifth parameter you can add a label which is tagged on every feature which has this adduct. This also determines the map number in the consensus file">
106 <sanitizer>
107 <valid initial="string.printable">
108 <remove value="'"/>
109 <remove value="&quot;"/>
110 </valid>
111 </sanitizer>
112 </param>
113 </repeat>
114 <param name="param_algorithm_MetaboliteFeatureDeconvolution_max_neutrals" type="integer" value="0" label="Maximal number of neutral adducts(q=0) allowed" help="(-max_neutrals) Add them in the 'potential_adducts' section!"/>
115 <param name="param_algorithm_MetaboliteFeatureDeconvolution_max_minority_bound" type="integer" min="0" optional="True" value="2" label="Maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant" help="(-max_minority_bound) E.g. setting this to 2 will not allow an adduct composition of '1(H+),3(Na+)' if Na+ is the least probable adduct"/>
116 <param name="param_algorithm_MetaboliteFeatureDeconvolution_min_rt_overlap" type="float" min="0.0" max="1.0" optional="True" value="0.66" label="Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)" help="(-min_rt_overlap) "/>
117 <param name="param_algorithm_MetaboliteFeatureDeconvolution_intensity_filter" display="radio" type="boolean" truevalue="-algorithm:MetaboliteFeatureDeconvolution:intensity_filter" falsevalue="" checked="false" optional="True" label="Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature" help="(-intensity_filter) It is not used for features of different charge"/>
118 <param name="param_algorithm_MetaboliteFeatureDeconvolution_negative_mode" type="text" size="30" value="false" label="Enable negative ionization mode" help="(-negative_mode) ">
119 <sanitizer>
120 <valid initial="string.printable">
121 <remove value="'"/>
122 <remove value="&quot;"/>
123 </valid>
124 </sanitizer>
125 </param>
126 <expand macro="advanced_options">
127 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
128 <param name="param_algorithm_MetaboliteFeatureDeconvolution_default_map_label" type="text" size="30" value="decharged features" label="Label of map in output consensus file where all features are put by default" help="(-default_map_label) ">
129 <sanitizer>
130 <valid initial="string.printable">
131 <remove value="'"/>
132 <remove value="&quot;"/>
133 </valid>
134 </sanitizer>
135 </param>
136 <param name="param_algorithm_MetaboliteFeatureDeconvolution_verbose_level" type="integer" min="0" max="3" optional="True" value="0" label="Amount of debug information given during processing" help="(-verbose_level) "/>
137 </expand>
138 </inputs>
139 <outputs>
140 <data name="param_out_cm" format="consensusxml"/>
141 <data name="param_out_fm" format="featurexml"/>
142 <data name="param_outpairs" format="consensusxml"/>
143 </outputs>
144 <help>Decharges and merges different feature charge variants of the same metabolite.
145
146
147 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaboliteAdductDecharger.html</help>
148 </tool>