Mercurial > repos > galaxyp > openms_fileinfo
diff FileInfo.xml @ 15:4af67edd5aef draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:16:37 +0000 |
| parents | e8dce5e07fa5 |
| children | 5a45e6ac9aae |
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--- a/FileInfo.xml Fri Nov 06 20:30:04 2020 +0000 +++ b/FileInfo.xml Thu Dec 01 19:16:37 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: [File Handling]--> -<tool id="FileInfo" name="FileInfo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="FileInfo" name="FileInfo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Shows basic information about the file, such as data ranges and file type.</description> <macros> <token name="@EXECUTABLE@">FileInfo</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -54,18 +52,18 @@ <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="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,trafoxml" optional="false" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,trafoxml data sets(s)"/> - <param name="m" argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/> - <param name="p" argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/> - <param name="s" argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/> - <param name="d" argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/> - <param name="c" argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/> - <param name="v" argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/> - <param name="i" argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/> + <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml" optional="false" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml data sets(s)"/> + <param argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/> + <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/> + <param argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/> + <param argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/> + <param argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/> + <param argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/> + <param argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/> <expand macro="adv_opts_macro"> - <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="-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"> @@ -82,13 +80,360 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_FileInfo"/> - <expand macro="manutest_FileInfo"/> + <tests><!-- TOPP_FileInfo_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_1_input.dta" ftype="dta"/> + <output name="out" file="FileInfo_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/> + <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_3 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_3_input.featureXML"/> + <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="true"/> + <param name="p" value="true"/> + <param name="s" value="true"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_4 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_4_input.mzXML"/> + <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="true"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_5 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_5_input.mzDat"/> + <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="true"/> + <param name="p" value="false"/> + <param name="s" value="true"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_6 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_6_input.mzData"/> + <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="true"/> + <param name="d" value="true"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_7 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_7_input.consensusXML"/> + <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="true"/> + <param name="p" value="true"/> + <param name="s" value="true"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_9 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_9_input.mzML"/> + <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="true"/> + <param name="p" value="true"/> + <param name="s" value="true"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_10 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_10_input.idXML"/> + <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_12 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_12_input.mzML"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="true"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_13 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_13_input.consensusXML"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_14 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_14_input.mzid"/> + <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="true"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_15 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_15_input.mzid"/> + <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="true"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_16 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_16_input.trafoXML"/> + <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_17 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_17_input.fasta"/> + <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FileInfo_18 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FileInfo_18_input.fasta"/> + <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="m" value="false"/> + <param name="p" value="false"/> + <param name="s" value="false"/> + <param name="d" value="false"/> + <param name="c" value="false"/> + <param name="v" value="false"/> + <param name="i" value="false"/> + <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[Shows basic information about the file, such as data ranges and file type. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FileInfo.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileInfo.html]]></help> <expand macro="references"/> </tool>