Mercurial > repos > galaxyp > openms_accuratemasssearch

comparison AccurateMassSearch.xml @ 12:40e0709178a5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:06:37 +0000
parents 96acf893530c
children 2dea459da18e
comparison
equal deleted inserted replaced
11:96acf893530c 12:40e0709178a5
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="AccurateMassSearch" name="AccurateMassSearch" version="2.3.0"> 4 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Match MS signals to molecules from a database by mass.</description> 5 <description>Match MS signals to molecules from a database by mass.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">AccurateMassSearch</token> 7 <token name="@EXECUTABLE@">AccurateMassSearch</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[AccurateMassSearch 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($in.ext)' &&
21 mkdir out &&
22 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir out_annotation &&
17 #end if 24 #end if
18 #if $param_out: 25 #if $positive_adducts:
19 -out $param_out 26 mkdir positive_adducts &&
27 ln -s '$positive_adducts' 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)' &&
20 #end if 28 #end if
21 #if $param_out_annotation: 29 #if $negative_adducts:
22 -out_annotation $param_out_annotation 30 mkdir negative_adducts &&
31 ln -s '$negative_adducts' 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)' &&
23 #end if 32 #end if
24 #if $param_positive_adducts: 33 #if $db.mapping:
25 -positive_adducts $param_positive_adducts 34 mkdir db.mapping &&
35 ${ ' '.join(["ln -s '%s' 'db.mapping/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _]) }
26 #end if 36 #end if
27 #if $param_negative_adducts: 37 #if $db.struct:
28 -negative_adducts $param_negative_adducts 38 mkdir db.struct &&
39 ${ ' '.join(["ln -s '%s' 'db.struct/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _]) }
29 #end if 40 #end if
30 -db:mapping 41
31 #for token in $param_db_mapping: 42 ## Main program call
32 $token 43
33 #end for 44 set -o pipefail &&
34 -db:struct 45 @EXECUTABLE@ -write_ctd ./ &&
35 #for token in $param_db_struct: 46 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
36 $token 47 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
37 #end for 48 -in
38 #if $param_algorithm_mass_error_value: 49 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
39 -algorithm:mass_error_value $param_algorithm_mass_error_value 50 -out
51 'out/output.${gxy2omsext("mztab")}'
52 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
53 -out_annotation
54 'out_annotation/output.${in.ext}'
40 #end if 55 #end if
41 #if $param_algorithm_mass_error_unit: 56 #if $positive_adducts:
42 -algorithm:mass_error_unit 57 -positive_adducts
43 #if " " in str($param_algorithm_mass_error_unit): 58 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)'
44 "$param_algorithm_mass_error_unit"
45 #else
46 $param_algorithm_mass_error_unit
47 #end if
48 #end if 59 #end if
49 #if $param_algorithm_ionization_mode: 60 #if $negative_adducts:
50 -algorithm:ionization_mode 61 -negative_adducts
51 #if " " in str($param_algorithm_ionization_mode): 62 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)'
52 "$param_algorithm_ionization_mode"
53 #else
54 $param_algorithm_ionization_mode
55 #end if
56 #end if 63 #end if
57 #if $param_algorithm_isotopic_similarity: 64 #if $db.mapping:
58 -algorithm:isotopic_similarity 65 -db:mapping
66 ${' '.join(["'db.mapping/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _])}
59 #end if 67 #end if
60 #if $param_algorithm_keep_unidentified_masses: 68 #if $db.struct:
61 -algorithm:keep_unidentified_masses 69 -db:struct
70 ${' '.join(["'db.struct/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _])}
62 #end if 71 #end if
63 #if $param_algorithm_mzTab_exportIsotopeIntensities: 72 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
64 -algorithm:mzTab:exportIsotopeIntensities $param_algorithm_mzTab_exportIsotopeIntensities 73 | tee '$stdout'
65 #end if 74 #end if
66 #if $adv_opts.adv_opts_selector=='advanced': 75
67 #if $adv_opts.param_force: 76 ## Postprocessing
68 -force 77 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
78 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
79 && mv 'out_annotation/output.${in.ext}' '$out_annotation'
69 #end if 80 #end if
70 #end if 81 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
71 ]]></command> 82 && mv '@EXECUTABLE@.ctd' '$ctd_out'
83 #end if]]></command>
84 <configfiles>
85 <inputs name="args_json" data_style="paths"/>
86 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
87 </configfiles>
72 <inputs> 88 <inputs>
73 <param name="param_in" type="data" format="featurexml,consensusxml" optional="False" label="featureXML or consensusXML file" help="(-in) "/> 89 <param name="in" argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="featureXML or consensusXML file" help=" select consensusxml,featurexml data sets(s)"/>
74 <param name="param_positive_adducts" type="data" format="tabular" optional="False" value="CHEMISTRY/PositiveAdducts.tsv" label="This file contains the list of potential positive adducts that will be looked for in the database" help="(-positive_adducts) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/> 90 <param name="positive_adducts" argument="-positive_adducts" type="data" format="tabular" optional="true" label="This file contains the list of potential positive adducts that will be looked for in the database" help="Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used select tabular data sets(s)"/>
75 <param name="param_negative_adducts" type="data" format="tabular" optional="False" value="CHEMISTRY/NegativeAdducts.tsv" label="This file contains the list of potential negative adducts that will be looked for in the database" help="(-negative_adducts) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/> 91 <param name="negative_adducts" argument="-negative_adducts" type="data" format="tabular" optional="true" label="This file contains the list of potential negative adducts that will be looked for in the database" help="Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used select tabular data sets(s)"/>
76 <param name="param_db_mapping" type="data" format="tabular" multiple="true" optional="False" size="30" value="CHEMISTRY/HMDBMappingFile.tsv" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="(-mapping) If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used"> 92 <section name="db" title="Database files which contain the identifications" help="" expanded="false">
77 <sanitizer> 93 <param name="mapping" argument="-db:mapping" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
78 <valid initial="string.printable"> 94 <param name="struct" argument="-db:struct" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
79 <remove value="'"/> 95 </section>
80 <remove value="&quot;"/> 96 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
81 </valid> 97 <param name="mass_error_value" argument="-algorithm:mass_error_value" type="float" optional="true" value="5.0" label="Tolerance allowed for accurate mass search" help=""/>
82 </sanitizer> 98 <param name="mass_error_unit" argument="-algorithm:mass_error_unit" display="radio" type="select" optional="false" label="Unit of mass error (ppm or Da)" help="">
99 <option value="ppm" selected="true">ppm</option>
100 <option value="Da">Da</option>
101 <expand macro="list_string_san"/>
102 </param>
103 <param name="ionization_mode" argument="-algorithm:ionization_mode" display="radio" type="select" optional="false" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
104 <option value="positive" selected="true">positive</option>
105 <option value="negative">negative</option>
106 <option value="auto">auto</option>
107 <expand macro="list_string_san"/>
108 </param>
109 <param name="isotopic_similarity" argument="-algorithm:isotopic_similarity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" help=""/>
110 <param name="use_feature_adducts" argument="-algorithm:use_feature_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to filter AMS candidates mismatching available feature adduct annotation" help=""/>
111 <param name="keep_unidentified_masses" argument="-algorithm:keep_unidentified_masses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep features that did not yield any DB hit" help=""/>
112 <section name="mzTab" title="" help="" expanded="false">
113 <param name="exportIsotopeIntensities" argument="-algorithm:mzTab:exportIsotopeIntensities" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[featureXML input only] Export column with available isotope trace intensities (opt_global_MTint)" help=""/>
114 </section>
115 </section>
116 <expand macro="adv_opts_macro">
117 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
118 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
119 <expand macro="list_string_san"/>
120 </param>
121 </expand>
122 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
123 <option value="out_annotation_FLAG">out_annotation ([featureXML input only] Export column with available isotope trace intensities (opt_global_MTint))</option>
124 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
83 </param> 125 </param>
84 <param name="param_db_struct" type="data" format="tabular" multiple="true" optional="False" size="30" value="CHEMISTRY/HMDB2StructMapping.tsv" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="(-struct) SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used">
85 <sanitizer>
86 <valid initial="string.printable">
87 <remove value="'"/>
88 <remove value="&quot;"/>
89 </valid>
90 </sanitizer>
91 </param>
92 <param name="param_algorithm_mass_error_value" type="float" value="5.0" label="Tolerance allowed for accurate mass search" help="(-mass_error_value) "/>
93 <param name="param_algorithm_mass_error_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) ">
94 <option value="ppm" selected="true">ppm</option>
95 <option value="Da">Da</option>
96 </param>
97 <param name="param_algorithm_ionization_mode" display="radio" type="select" optional="False" value="positive" label="Positive or negative ionization mode?" help="(-ionization_mode) If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
98 <option value="positive" selected="true">positive</option>
99 <option value="negative">negative</option>
100 <option value="auto">auto</option>
101 </param>
102 <param name="param_algorithm_isotopic_similarity" display="radio" type="boolean" truevalue="-algorithm:isotopic_similarity" falsevalue="" checked="false" optional="True" label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" help="(-isotopic_similarity) "/>
103 <param name="param_algorithm_keep_unidentified_masses" display="radio" type="boolean" truevalue="-algorithm:keep_unidentified_masses" falsevalue="" checked="false" optional="True" label="Keep features that did not yield any DB hit" help="(-keep_unidentified_masses) "/>
104 <param name="param_algorithm_mzTab_exportIsotopeIntensities" type="integer" min="0" optional="True" value="0" label="[featureXML input only] Number of extra columns in mzTab output, which provide intensities up to the x'th isotope" help="(-exportIsotopeIntensities) '0' to deactivate, '1' for monoisotopic peak, etc. If a feature does not have a certain isotope, 'null' will be reported"/>
105 <expand macro="advanced_options">
106 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
107 </expand>
108 </inputs> 126 </inputs>
109 <outputs> 127 <outputs>
110 <data name="param_out" format="tabular"/> 128 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
111 <data name="param_out_annotation" metadata_source="param_in" format="input"/> 129 <data name="out_annotation" label="${tool.name} on ${on_string}: out_annotation" format_source="in" metadata_source="in">
130 <filter>OPTIONAL_OUTPUTS is not None and "out_annotation_FLAG" in OPTIONAL_OUTPUTS</filter>
131 </data>
132 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
133 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
134 </data>
112 </outputs> 135 </outputs>
113 <help>Match MS signals to molecules from a database by mass. 136 <tests>
137 <expand macro="autotest_AccurateMassSearch"/>
138 <expand macro="manutest_AccurateMassSearch"/>
139 </tests>
140 <help><![CDATA[Match MS signals to molecules from a database by mass.
114 141
115 142
116 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_AccurateMassSearch.html</help> 143 For more information, visit http://www.openms.de/documentation/UTILS_AccurateMassSearch.html]]></help>
144 <expand macro="references"/>
117 </tool> 145 </tool>