Mercurial > repos > galaxyp > openms_metaboliteadductdecharger

comparison MetaboliteAdductDecharger.xml @ 4:68e3317532cb draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:01:24 +0000
parents d37e3dc967b9
children ebc51eae71cd
comparison
equal deleted inserted replaced
3:65db7655c6a2 4:68e3317532cb
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 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]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MetaboliteAdductDecharger" name="MetaboliteAdductDecharger" version="2.3.0"> 4 <tool id="MetaboliteAdductDecharger" name="MetaboliteAdductDecharger" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Decharges and merges different feature charge variants of the same metabolite.</description> 5 <description>Decharges and merges different feature charge variants of the same metabolite.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MetaboliteAdductDecharger</token> 7 <token name="@EXECUTABLE@">MetaboliteAdductDecharger</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[MetaboliteAdductDecharger 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir out_cm &&
22 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir out_fm &&
17 #end if 24 #end if
18 #if $param_out_cm: 25 #if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
19 -out_cm $param_out_cm 26 mkdir outpairs &&
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 27 #end if
53 28
54 #if $rep_param_algorithm_MetaboliteFeatureDeconvolution_potential_adducts: 29 ## Main program call
55 -algorithm:MetaboliteFeatureDeconvolution:potential_adducts 30
56 #for token in $rep_param_algorithm_MetaboliteFeatureDeconvolution_potential_adducts: 31 set -o pipefail &&
57 #if " " in str(token): 32 @EXECUTABLE@ -write_ctd ./ &&
58 "$token.param_algorithm_MetaboliteFeatureDeconvolution_potential_adducts" 33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
59 #else 34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
60 $token.param_algorithm_MetaboliteFeatureDeconvolution_potential_adducts 35 -in
61 #end if 36 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
62 #end for 37 -out_cm
38 'out_cm/output.${gxy2omsext("consensusxml")}'
39 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
40 -out_fm
41 'out_fm/output.${gxy2omsext("featurexml")}'
63 #end if 42 #end if
64 #if $param_algorithm_MetaboliteFeatureDeconvolution_max_neutrals: 43 #if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
65 -algorithm:MetaboliteFeatureDeconvolution:max_neutrals $param_algorithm_MetaboliteFeatureDeconvolution_max_neutrals 44 -outpairs
45 'outpairs/output.${gxy2omsext("consensusxml")}'
66 #end if 46 #end if
67 #if $param_algorithm_MetaboliteFeatureDeconvolution_max_minority_bound: 47 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
68 -algorithm:MetaboliteFeatureDeconvolution:max_minority_bound $param_algorithm_MetaboliteFeatureDeconvolution_max_minority_bound 48 | tee '$stdout'
69 #end if 49 #end if
70 #if $param_algorithm_MetaboliteFeatureDeconvolution_min_rt_overlap: 50
71 -algorithm:MetaboliteFeatureDeconvolution:min_rt_overlap $param_algorithm_MetaboliteFeatureDeconvolution_min_rt_overlap 51 ## Postprocessing
52 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
53 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
54 && mv 'out_fm/output.${gxy2omsext("featurexml")}' '$out_fm'
72 #end if 55 #end if
73 #if $param_algorithm_MetaboliteFeatureDeconvolution_intensity_filter: 56 #if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
74 -algorithm:MetaboliteFeatureDeconvolution:intensity_filter 57 && mv 'outpairs/output.${gxy2omsext("consensusxml")}' '$outpairs'
75 #end if 58 #end if
76 #if $param_algorithm_MetaboliteFeatureDeconvolution_negative_mode: 59 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
77 -algorithm:MetaboliteFeatureDeconvolution:negative_mode "$param_algorithm_MetaboliteFeatureDeconvolution_negative_mode" 60 && mv '@EXECUTABLE@.ctd' '$ctd_out'
78 #end if 61 #end if]]></command>
79 #if $adv_opts.adv_opts_selector=='advanced': 62 <configfiles>
80 #if $adv_opts.param_force: 63 <inputs name="args_json" data_style="paths"/>
81 -force 64 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
82 #end if 65 </configfiles>
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> 66 <inputs>
92 <param name="param_in" type="data" format="featurexml" optional="False" label="input file" help="(-in) "/> 67 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="input file" help=" select featurexml data sets(s)"/>
93 <param name="param_algorithm_MetaboliteFeatureDeconvolution_charge_min" type="integer" value="1" label="Minimal possible charge" help="(-charge_min) "/> 68 <section name="algorithm" title="Feature decharging algorithm section" help="" expanded="false">
94 <param name="param_algorithm_MetaboliteFeatureDeconvolution_charge_max" type="integer" value="3" label="Maximal possible charge" help="(-charge_max) "/> 69 <section name="MetaboliteFeatureDeconvolution" title="" help="" expanded="false">
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"/> 70 <param name="charge_min" argument="-algorithm:MetaboliteFeatureDeconvolution:charge_min" type="integer" optional="true" value="1" label="Minimal possible charge" help=""/>
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) "> 71 <param name="charge_max" argument="-algorithm:MetaboliteFeatureDeconvolution:charge_max" type="integer" optional="true" value="3" label="Maximal possible charge" help=""/>
97 <option value="feature" selected="true">feature</option> 72 <param name="charge_span_max" argument="-algorithm:MetaboliteFeatureDeconvolution:charge_span_max" type="integer" optional="true" min="1" value="3" label="Maximal range of charges for a single analyte" help="i.e. observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge"/>
98 <option value="heuristic">heuristic</option> 73 <param name="q_try" argument="-algorithm:MetaboliteFeatureDeconvolution:q_try" display="radio" type="select" optional="false" 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="">
99 <option value="all">all</option> 74 <option value="feature" selected="true">feature</option>
75 <option value="heuristic">heuristic</option>
76 <option value="all">all</option>
77 <expand macro="list_string_san"/>
78 </param>
79 <param name="retention_max_diff" argument="-algorithm:MetaboliteFeatureDeconvolution:retention_max_diff" type="float" optional="true" value="1.0" label="Maximum allowed RT difference between any two features if their relation shall be determined" help=""/>
80 <param name="retention_max_diff_local" argument="-algorithm:MetaboliteFeatureDeconvolution:retention_max_diff_local" type="float" optional="true" 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=""/>
81 <param name="mass_max_diff" argument="-algorithm:MetaboliteFeatureDeconvolution:mass_max_diff" type="float" optional="true" min="0.0" value="0.05" label="Maximum allowed mass tolerance per feature" help="Defines a symmetric tolerance window around the feature. When looking at possible feature pairs, the allowed feature-wise errors are combined for consideration of possible adduct shifts. For ppm tolerances, each window is based on the respective observed feature mz (instead of putative experimental mzs causing the observed one)!"/>
82 <param name="unit" argument="-algorithm:MetaboliteFeatureDeconvolution:unit" display="radio" type="select" optional="false" label="Unit of the 'max_difference' paramete" help="">
83 <option value="Da" selected="true">Da</option>
84 <option value="ppm">ppm</option>
85 <expand macro="list_string_san"/>
86 </param>
87 <param name="potential_adducts" argument="-algorithm:MetaboliteFeatureDeconvolution:potential_adducts" type="text" optional="true" value="H:+:0.4 Na:+:0.25 NH4:+:0.25 K:+:0.1 H-2O-1:0:0.05" label="Adducts used to explain mass differences in format: 'Elements:Charge(+/-/0):Probability[:RTShift[:Label]]'" help="i.e. the number of '+' or '-' indicate the charge ('0' if neutral adduct), e.g. 'Ca:++:0.5' indicates +2. Probabilites have to be in (0,1]. The optional RTShift param 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 fifth parameter you can add a label for every feature with this adduct. This also determines the map number in the consensus file. Adduct element losses are written in the form 'H-2'. All provided adducts need to have the same charge sign or be neutral! Mixing of adducts with different charge directions is only allowed as neutral complexes. For example, 'H-1Na:0:0.05' can be used to model Sodium gains (with balancing deprotonation) in negative mode (space separated list, in order to allow for spaces in list items surround them by single quotes)">
88 <expand macro="list_string_val"/>
89 <expand macro="list_string_san"/>
90 </param>
91 <param name="max_neutrals" argument="-algorithm:MetaboliteFeatureDeconvolution:max_neutrals" type="integer" optional="true" value="1" label="Maximal number of neutral adducts(q=0) allowed" help="Add them in the 'potential_adducts' section!"/>
92 <param name="use_minority_bound" argument="-algorithm:MetaboliteFeatureDeconvolution:use_minority_bound" type="text" optional="true" value="true" label="Prune the considered adduct transitions by transition probabilities" help="">
93 <expand macro="list_string_san"/>
94 </param>
95 <param name="max_minority_bound" argument="-algorithm:MetaboliteFeatureDeconvolution:max_minority_bound" type="integer" optional="true" min="0" value="3" label="Limits allowed adduct compositions and changes between compositions in the underlying graph optimization problem by introducing a probability-based threshold: the minority bound sets the maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant with maximum charge only containing the most likely adduct otherwise" help="E.g., for 'charge_max' 4 and 'max_minority_bound' 2 with most probable adduct being H+ and least probable adduct being Na+, this will allow adduct compositions of '2(H+),2(Na+)' but not of '1(H+),3(Na+)'. Further, adduct compositions/changes less likely than '2(H+),2(Na+)' will be discarded as well"/>
96 <param name="min_rt_overlap" argument="-algorithm:MetaboliteFeatureDeconvolution:min_rt_overlap" type="float" optional="true" min="0.0" max="1.0" value="0.66" label="Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)" help=""/>
97 <param name="intensity_filter" argument="-algorithm:MetaboliteFeatureDeconvolution:intensity_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" 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="It is not used for features of different charge"/>
98 <param name="negative_mode" argument="-algorithm:MetaboliteFeatureDeconvolution:negative_mode" type="text" optional="true" value="false" label="Enable negative ionization mode" help="">
99 <expand macro="list_string_san"/>
100 </param>
101 <param name="default_map_label" argument="-algorithm:MetaboliteFeatureDeconvolution:default_map_label" type="text" optional="true" value="decharged features" label="Label of map in output consensus file where all features are put by default" help="">
102 <expand macro="list_string_san"/>
103 </param>
104 <param name="verbose_level" argument="-algorithm:MetaboliteFeatureDeconvolution:verbose_level" type="integer" optional="true" min="0" max="3" value="0" label="Amount of debug information given during processing" help=""/>
105 </section>
106 </section>
107 <expand macro="adv_opts_macro">
108 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
109 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
110 <expand macro="list_string_san"/>
111 </param>
112 </expand>
113 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
114 <option value="out_fm_FLAG">out_fm (Amount of debug information given during processing)</option>
115 <option value="outpairs_FLAG">outpairs (Amount of debug information given during processing)</option>
116 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
100 </param> 117 </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> 118 </inputs>
139 <outputs> 119 <outputs>
140 <data name="param_out_cm" format="consensusxml"/> 120 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml"/>
141 <data name="param_out_fm" format="featurexml"/> 121 <data name="out_fm" label="${tool.name} on ${on_string}: out_fm" format="featurexml">
142 <data name="param_outpairs" format="consensusxml"/> 122 <filter>OPTIONAL_OUTPUTS is not None and "out_fm_FLAG" in OPTIONAL_OUTPUTS</filter>
123 </data>
124 <data name="outpairs" label="${tool.name} on ${on_string}: outpairs" format="consensusxml">
125 <filter>OPTIONAL_OUTPUTS is not None and "outpairs_FLAG" in OPTIONAL_OUTPUTS</filter>
126 </data>
127 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
128 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
129 </data>
143 </outputs> 130 </outputs>
144 <help>Decharges and merges different feature charge variants of the same metabolite. 131 <tests>
132 <expand macro="autotest_MetaboliteAdductDecharger"/>
133 <expand macro="manutest_MetaboliteAdductDecharger"/>
134 </tests>
135 <help><![CDATA[Decharges and merges different feature charge variants of the same metabolite.
145 136
146 137
147 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MetaboliteAdductDecharger.html</help> 138 For more information, visit http://www.openms.de/documentation/UTILS_MetaboliteAdductDecharger.html]]></help>
139 <expand macro="references"/>
148 </tool> 140 </tool>