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comparison AccurateMassSearch.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="1.12.0"> 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 <description>Find potential HMDB ids within the given mass error window.</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.0.0">
5 <token name="@EXECUTABLE@">AccurateMassSearch</token> 5 <description>Find potential HMDB ids within the given mass error window.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">AccurateMassSearch</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>AccurateMassSearch 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>AccurateMassSearch
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -out_annotation ${param_out_annotation} 17 #end if
15 -positive_adducts_file ${param_positive_adducts_file} 18 #if $param_out:
16 -negative_adducts_file ${param_negative_adducts_file} 19 -out $param_out
17 -threads \${GALAXY_SLOTS:-24} 20 #end if
18 -db:mapping ${param_mapping} 21 #if $param_out_annotation:
19 -db:struct ${param_struct} 22 -out_annotation $param_out_annotation
20 -algorithm:mass_error_value ${param_mass_error_value} 23 #end if
21 -algorithm:mass_error_unit ${param_mass_error_unit} 24 #if $param_positive_adducts_file:
22 -algorithm:ionization_mode ${param_ionization_mode} 25 -positive_adducts_file $param_positive_adducts_file
23 ${param_isotopic_similarity} 26 #end if
24 -algorithm:report_mode ${param_report_mode} 27 #if $param_negative_adducts_file:
28 -negative_adducts_file $param_negative_adducts_file
29 #end if
30 -threads \${GALAXY_SLOTS:-24}
31 #if $param_db_mapping:
32 -db:mapping $param_db_mapping
33 #end if
34 #if $param_db_struct:
35 -db:struct $param_db_struct
36 #end if
37 #if $param_algorithm_mass_error_value:
38 -algorithm:mass_error_value $param_algorithm_mass_error_value
39 #end if
40 #if $param_algorithm_mass_error_unit:
41 -algorithm:mass_error_unit
42 #if &quot; &quot; in str($param_algorithm_mass_error_unit):
43 &quot;$param_algorithm_mass_error_unit&quot;
44 #else
45 $param_algorithm_mass_error_unit
46 #end if
47 #end if
48 #if $param_algorithm_ionization_mode:
49 -algorithm:ionization_mode
50 #if &quot; &quot; in str($param_algorithm_ionization_mode):
51 &quot;$param_algorithm_ionization_mode&quot;
52 #else
53 $param_algorithm_ionization_mode
54 #end if
55 #end if
56 #if $param_algorithm_isotopic_similarity:
57 -algorithm:isotopic_similarity
58 #end if
59 #if $param_algorithm_keep_unidentified_masses:
60 -algorithm:keep_unidentified_masses
61 #end if
62 #if $param_algorithm_mzTab_exportIsotopeIntensities:
63 -algorithm:mzTab:exportIsotopeIntensities $param_algorithm_mzTab_exportIsotopeIntensities
64 #end if
65 #if $adv_opts.adv_opts_selector=='advanced':
66 #if $adv_opts.param_force:
67 -force
68 #end if
69 #end if
25 </command> 70 </command>
26 <inputs> 71 <inputs>
27 <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" label="featureXML or consensusXML file" help="(-in)"/> 72 <param format="xml,consensusxml" help="(-in) " label="featureXML or consensusXML file" name="param_in" optional="False" type="data"/>
28 <param name="param_positive_adducts_file" type="data" format="" optional="False" value="CHEMISTRY/PositiveAdducts.tsv" label="This file contains the list of potential positive adducts that will be looked for in the database. 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." help="(-positive_adducts_file)"/> 73 <param format="tabular" help="(-positive_adducts_file) 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" label="This file contains the list of potential positive adducts that will be looked for in the database" name="param_positive_adducts_file" optional="False" type="data" value="CHEMISTRY/PositiveAdducts.tsv"/>
29 <param name="param_negative_adducts_file" type="data" format="" optional="False" value="CHEMISTRY/NegativeAdducts.tsv" label="This file contains the list of potential negative adducts that will be looked for in the database. 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." help="(-negative_adducts_file)"/> 74 <param format="tabular" help="(-negative_adducts_file) 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" label="This file contains the list of potential negative adducts that will be looked for in the database" name="param_negative_adducts_file" optional="False" type="data" value="CHEMISTRY/NegativeAdducts.tsv"/>
30 <param name="param_mapping" type="data" format="" optional="False" value="CHEMISTRY/HMDBMappingFile.tsv" label="Database input file, containing three tab-separated columns of mass, formula, identifier. 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." help="(-mapping)"/> 75 <param format="tabular" 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" label="Database input file, containing three tab-separated columns of mass, formula, identifie" name="param_db_mapping" optional="False" type="data" value="CHEMISTRY/HMDBMappingFile.tsv"/>
31 <param name="param_struct" type="data" format="" optional="False" value="CHEMISTRY/HMDB2StructMapping.tsv" label="Database input file, containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file. 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." help="(-struct)"/> 76 <param format="tabular" 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" label="Database input file, containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" name="param_db_struct" optional="False" type="data" value="CHEMISTRY/HMDB2StructMapping.tsv"/>
32 <param name="param_mass_error_value" type="float" value="5.0" label="Tolerance allowed for accurate mass search." help="(-mass_error_value)"/> 77 <param help="(-mass_error_value) " label="Tolerance allowed for accurate mass search" name="param_algorithm_mass_error_value" type="float" value="5.0"/>
33 <param name="param_mass_error_unit" type="select" optional="True" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit)"> 78 <param help="(-mass_error_unit) " label="Unit of mass error (ppm or Da)" name="param_algorithm_mass_error_unit" optional="True" type="select" value="ppm">
34 <option value="ppm">ppm</option> 79 <option value="ppm">ppm</option>
35 <option value="Da">Da</option> 80 <option value="Da">Da</option>
36 </param> 81 </param>
37 <param name="param_ionization_mode" type="select" optional="True" value="positive" label="Positive or negative 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." help="(-ionization_mode)"> 82 <param 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" label="Positive or negative ionization mode?" name="param_algorithm_ionization_mode" optional="True" type="select" value="positive">
38 <option value="positive">positive</option> 83 <option value="positive">positive</option>
39 <option value="negative">negative</option> 84 <option value="negative">negative</option>
40 <option value="auto">auto</option> 85 <option value="auto">auto</option>
41 </param> 86 </param>
42 <param name="param_isotopic_similarity" type="boolean" truevalue="-algorithm:isotopic_similarity true" falsevalue="-algorithm:isotopic_similarity false" 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)"/> 87 <param checked="false" falsevalue="" help="(-isotopic_similarity) " label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" name="param_algorithm_isotopic_similarity" optional="True" truevalue="-algorithm:isotopic_similarity" type="boolean"/>
43 <param name="param_report_mode" type="select" optional="True" value="all" label="Results are reported in one of several modes: Either (all) matching hits, the (top3) scoring hits, or the (best) scoring hit." help="(-report_mode)"> 88 <param checked="false" falsevalue="" help="(-keep_unidentified_masses) " label="Keep features that did not yield any DB hit" name="param_algorithm_keep_unidentified_masses" optional="True" truevalue="-algorithm:keep_unidentified_masses" type="boolean"/>
44 <option value="all">all</option> 89 <param help="(-exportIsotopeIntensities) '0' to deactivate, '1' for monoisotopic peak, etc. If a feature does not have a certain isotope, 'null' will be reported" label="[featureXML input only] Number of extra columns in mzTab output, which provide intensities up to the x'th isotope" min="0" name="param_algorithm_mzTab_exportIsotopeIntensities" optional="True" type="integer" value="0"/>
45 <option value="top3">top3</option> 90 <expand macro="advanced_options">
46 <option value="best">best</option> 91 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
47 </param> 92 </expand>
48 </inputs> 93 </inputs>
49 <outputs> 94 <outputs>
50 <data name="param_out" label="mzTab file" format="tabular"/> 95 <data format="tabular" name="param_out"/>
51 <data name="param_out_annotation" label="The input file, annotated with matching hits from the database." format="consensusXML"> 96 <data format="input" metadata_source="param_in" name="param_out_annotation"/>
52 <change_format> 97 </outputs>
53 <when input="param_out_type" value="featureXML" format="featureXML"/> 98 <help>Find potential HMDB ids within the given mass error window.
54 </change_format>
55 </data>
56 </outputs>
57 <help>**What it does**
58
59 Find potential HMDB ids within the given mass error window.
60 99
61 100
62 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html 101 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html</help>
63 102 </tool>
64 @REFERENCES@
65 </help>
66 </tool>