Mercurial > repos > galaxyp > openms_targetedfileconverter
diff TargetedFileConverter.xml @ 11:9c70a651a53e draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:21:24 +0000 |
| parents | 6562463bf496 |
| children |
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--- a/TargetedFileConverter.xml Fri Nov 06 20:02:35 2020 +0000 +++ b/TargetedFileConverter.xml Thu Dec 01 19:21:24 2022 +0000 @@ -1,13 +1,11 @@ <?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: [Targeted Experiments]--> -<tool id="TargetedFileConverter" name="TargetedFileConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="TargetedFileConverter" name="TargetedFileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Converts different transition files for targeted proteomics / metabolomics analysis.</description> <macros> <token name="@EXECUTABLE@">TargetedFileConverter</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,28 +39,28 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file select mrm,pqp,tabular,traml data sets(s)"/> - <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: not all conversion paths work or make sense"> + <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file select mrm,pqp,tabular,traml data sets(s)"/> + <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: not all conversion paths work or make sense"> <option value="TraML">traml</option> <option value="pqp">pqp</option> <option value="tsv">tabular (tsv)</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="out_type"/> </param> <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> - <param name="retentionTimeInterpretation" argument="-algorithm:retentionTimeInterpretation" display="radio" type="select" optional="false" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help=""> + <param name="retentionTimeInterpretation" argument="-algorithm:retentionTimeInterpretation" type="select" optional="true" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help=""> <option value="iRT" selected="true">iRT</option> <option value="seconds">seconds</option> <option value="minutes">minutes</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="retentionTimeInterpretation"/> </param> <param name="override_group_label_check" argument="-algorithm:override_group_label_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="Only turn this off if you know what you are doing"/> <param name="force_invalid_mods" argument="-algorithm:force_invalid_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help=""/> </section> <expand macro="adv_opts_macro"> - <param name="legacy_traml_id" argument="-legacy_traml_id" type="boolean" truevalue="true" falsevalue="false" checked="false" label="PQP to TraML: Should legacy TraML IDs be used?" help=""/> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <param argument="-legacy_traml_id" type="boolean" truevalue="true" falsevalue="false" checked="false" label="PQP to TraML: Should legacy TraML IDs be used?" help=""/> + <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> + <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -70,9 +68,8 @@ </param> </inputs> <outputs> - <data name="out" label="${tool.name} on ${on_string}: out"> + <data name="out" label="${tool.name} on ${on_string}: out" format="traml"> <change_format> - <when input="out_type" value="TraML" format="traml"/> <when input="out_type" value="pqp" format="pqp"/> <when input="out_type" value="tsv" format="tabular"/> </change_format> @@ -81,13 +78,450 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_TargetedFileConverter"/> - <expand macro="manutest_TargetedFileConverter"/> + <tests><!-- TOPP_ConvertTSVToTraML_test_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/> + <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ConvertTSVToTraML_test_2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> + <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="minutes"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ConvertTSVToTraML_test_3 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> + <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="seconds"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ConvertTSVToTraML_test_4 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/> + <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ConvertTSVToTraML_test_5 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/> + <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ConvertTSVToTraML_test_6 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/> + <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ConvertTSVToTraML_test_7 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/> + <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_TargetedFileConverter_test_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_TargetedFileConverter_test_2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_TargetedFileConverter_test_3 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_TargetedFileConverter_test_4 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="true"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_TargetedFileConverter_test_10 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/> + <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <param name="out_type" value="tsv"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_TargetedFileConverter_test_11 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_TargetedFileConverter_test_8 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/> + <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <param name="out_type" value="tsv"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="true"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_TargetedFileConverter_test_9 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="true"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_TargetedFileConverter_test_5 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ConvertTSVToTraML_output.TraML"/> + <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <param name="out_type" value="tsv"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_TargetedFileConverter_test_12 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/> + <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="true"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_TargetedFileConverter_test_13 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/> + <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_TargetedFileConverter_test_6 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ConvertTSVToTraML_5_output.TraML"/> + <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <param name="out_type" value="tsv"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- UTILS_AssayGeneratorMetabo_6 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="legacy_traml_id" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/> + <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <param name="out_type" value="TraML"/> + <section name="algorithm"> + <param name="retentionTimeInterpretation" value="iRT"/> + <param name="override_group_label_check" value="false"/> + <param name="force_invalid_mods" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Converts different transition files for targeted proteomics / metabolomics analysis. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_TargetedFileConverter.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TargetedFileConverter.html]]></help> <expand macro="references"/> </tool>