comparison AccurateMassSearch.xml @ 12:4f9d07638178 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

11:52767a904430

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.2.0">
  <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="references"/>
  <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
-db:mapping
  #for token in $param_db_mapping:
    $token
  #end for

#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" 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">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>

  </inputs>
  <outputs>
    <data name="param_out" format="tabular"/>
    <data name="param_out_annotation" metadata_source="param_in" format="input"/>
  </outputs>
  <help>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>
</tool>

12:4f9d07638178

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.3.0">
  <description>Match MS signals to molecules from a database by mass.</description>
  <macros>
    <token name="@EXECUTABLE@">AccurateMassSearch</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[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:
  -positive_adducts $param_positive_adducts
#end if
#if $param_negative_adducts:
  -negative_adducts $param_negative_adducts
#end if
-db:mapping
  #for token in $param_db_mapping:
    $token
  #end for

#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" 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"/>
    <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"/>
    <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">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>

  </inputs>
  <outputs>
    <data name="param_out" format="tabular"/>
    <data name="param_out_annotation" metadata_source="param_in" format="input"/>
  </outputs>
  <help>Match MS signals to molecules from a database by mass.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_AccurateMassSearch.html</help>
</tool>