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diff AccurateMassSearch.xml @ 0:3070d71e0e5c draft
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author | bgruening |
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date | Thu, 16 Apr 2015 08:37:04 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AccurateMassSearch.xml Thu Apr 16 08:37:04 2015 -0400 @@ -0,0 +1,111 @@ +<?xml version='1.0' encoding='UTF-8'?> +<tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.0.0"> + <description>Find potential HMDB ids within the given mass error window.</description> + <macros> + <token name="@EXECUTABLE@">AccurateMassSearch</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>AccurateMassSearch + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_annotation: + -out_annotation $param_out_annotation +#end if +#if $param_positive_adducts_file: + -positive_adducts_file $param_positive_adducts_file +#end if +#if $param_negative_adducts_file: + -negative_adducts_file $param_negative_adducts_file +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_db_mapping: + -db:mapping $param_db_mapping +#end if +#if $param_db_struct: + -db:struct $param_db_struct +#end if +#if $param_algorithm_mass_error_value: + -algorithm:mass_error_value $param_algorithm_mass_error_value +#end if +#if $param_algorithm_mass_error_unit: + -algorithm:mass_error_unit + #if " " in str($param_algorithm_mass_error_unit): + "$param_algorithm_mass_error_unit" + #else + $param_algorithm_mass_error_unit + #end if +#end if +#if $param_algorithm_ionization_mode: + -algorithm:ionization_mode + #if " " in str($param_algorithm_ionization_mode): + "$param_algorithm_ionization_mode" + #else + $param_algorithm_ionization_mode + #end if +#end if +#if $param_algorithm_isotopic_similarity: + -algorithm:isotopic_similarity +#end if +#if $param_algorithm_report_mode: + -algorithm:report_mode + #if " " in str($param_algorithm_report_mode): + "$param_algorithm_report_mode" + #else + $param_algorithm_report_mode + #end if +#end if +#if $param_algorithm_keep_unidentified_masses: + -algorithm:keep_unidentified_masses +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if +</command> + <inputs> + <param name="param_in" type="data" format="featurexml,consensusxml" optional="False" label="featureXML or consensusXML file" help="(-in) "/> + <param name="param_positive_adducts_file" 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_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"/> + <param name="param_negative_adducts_file" 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_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"/> + <param name="param_db_mapping" type="data" format="tabular" optional="False" value="CHEMISTRY/HMDBMappingFile.tsv" label="Database input file, 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"/> + <param name="param_db_struct" type="data" format="tabular" 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" 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"/> + <param name="param_algorithm_mass_error_value" type="float" value="5.0" label="Tolerance allowed for accurate mass search" help="(-mass_error_value) "/> + <param name="param_algorithm_mass_error_unit" type="select" optional="True" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) "> + <option value="ppm">ppm</option> + <option value="Da">Da</option> + </param> + <param name="param_algorithm_ionization_mode" type="select" optional="True" 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"> + <option value="positive">positive</option> + <option value="negative">negative</option> + <option value="auto">auto</option> + </param> + <param name="param_algorithm_isotopic_similarity" 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) "/> + <param name="param_algorithm_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) "> + <option value="all">all</option> + <option value="top3">top3</option> + <option value="best">best</option> + </param> + <param name="param_algorithm_keep_unidentified_masses" 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) "/> + <expand macro="advanced_options"> + <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + </expand> + </inputs> + <outputs> + <data name="param_out" format="tabular"/> + <data name="param_out_annotation" metadata_source="param_in" format="input"/> + </outputs> + <help>**What it does** + +Find potential HMDB ids within the given mass error window. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html</help> + <expand macro="references"/> +</tool>