Mercurial > repos > galaxyp > openms_qccalculator
diff QCCalculator.xml @ 13:d0607dfea8fa draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:09:47 +0000 |
| parents | 044adca691a7 |
| children | f6f07c3e99a2 |
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--- a/QCCalculator.xml Fri Nov 06 19:41:42 2020 +0000 +++ b/QCCalculator.xml Thu Dec 01 19:09:47 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: [Utilities]--> -<tool id="QCCalculator" name="QCCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="QCCalculator" name="QCCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.</description> <macros> <token name="@EXECUTABLE@">QCCalculator</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,7 +39,7 @@ -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' -out -'out/output.${gxy2omsext("qcml")}' +'out/output.${out_type}' #if $id: -id 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' @@ -56,7 +54,7 @@ #end if ## Postprocessing -&& mv 'out/output.${gxy2omsext("qcml")}' '$out' +&& mv 'out/output.${out_type}' '$out' #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv '@EXECUTABLE@.ctd' '$ctd_out' #end if]]></command> @@ -65,15 +63,32 @@ <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="mzml" optional="false" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help=" select mzml data sets(s)"/> - <param name="id" argument="-id" type="data" format="idxml" optional="true" label="Input idXML file containing the identifications" help="Your identifications will be exported in an easy-to-read format select idxml data sets(s)"/> - <param name="feature" argument="-feature" type="data" format="featurexml" optional="true" label="feature input file (this is relevant for most QC issues)" help=" select featurexml data sets(s)"/> - <param name="consensus" argument="-consensus" type="data" format="consensusxml" optional="true" label="consensus input file (this is only used for charge state deconvoluted output" help="Use the consensusXML output form the DeCharger) select consensusxml data sets(s)"/> - <param name="remove_duplicate_features" argument="-remove_duplicate_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="This flag should be set, if you work with a set of merged features" help=""/> + <param argument="-in" type="data" format="mzml" optional="false" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help=" select mzml 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=""> + <option value="mzQC">mzqc</option> + <option value="qcML">qcml</option> + <expand macro="list_string_san" name="out_type"/> + </param> + <param argument="-label" type="text" optional="true" value="label" label="unique name for the run that can be used in a figure label" help=""> + <expand macro="list_string_san" name="label"/> + </param> + <param argument="-name" type="text" optional="true" value="" label="name of the person creating this mzQC file" help=""> + <expand macro="list_string_san" name="name"/> + </param> + <param argument="-address" type="text" optional="true" value="" label="contact address (mail/e-mail or phone)" help=""> + <expand macro="list_string_san" name="address"/> + </param> + <param argument="-description" type="text" optional="true" value="" label="description and comments about the mzQC file contents" help=""> + <expand macro="list_string_san" name="description"/> + </param> + <param argument="-id" type="data" format="idxml" optional="true" label="Input idXML file containing the identifications" help="Your identifications will be exported in an easy-to-read format select idxml data sets(s)"/> + <param argument="-feature" type="data" format="featurexml" optional="true" label="feature input file (this is relevant for most QC issues)" help=" select featurexml data sets(s)"/> + <param argument="-consensus" type="data" format="consensusxml" optional="true" label="consensus input file (this is only used for charge state deconvoluted output" help="Use the consensusXML output form the DeCharger) select consensusxml data sets(s)"/> + <param argument="-remove_duplicate_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="This flag should be set, if you work with a set of merged features" 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"> @@ -81,18 +96,85 @@ </param> </inputs> <outputs> - <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="mzqc"> + <change_format> + <when input="out_type" value="qcML" format="qcml"/> + </change_format> + </data> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_QCCalculator"/> - <expand macro="manutest_QCCalculator"/> - </tests> + <tests><!-- UTILS_QCCalculator_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="QCCalculator_input.mzML"/> + <output name="out" file="QCCalculator_1.qcML" compare="sim_size" delta_frac="0.7" ftype="qcml"/> + <param name="out_type" value="qcML"/> + <param name="label" value="label"/> + <param name="name" value=""/> + <param name="address" value=""/> + <param name="description" value=""/> + <param name="remove_duplicate_features" 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> + <!-- UTILS_QCCalculator_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="QCCalculator_input.mzML"/> + <output name="out" file="QCCalculator_2.mzQC" compare="sim_size" delta_frac="0.7" ftype="mzqc"/> + <param name="out_type" value="mzQC"/> + <param name="label" value="label"/> + <param name="name" value="name"/> + <param name="address" value="address"/> + <param name="description" value="description"/> + <param name="id" value="OpenPepXL_output.idXML"/> + <param name="feature" value="FeatureFinderMetaboIdent_1_output.featureXML"/> + <param name="remove_duplicate_features" 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> + <test expect_num_outputs="1"><!-- took test data from another test w mzML input --> + <param name="adv_opts|test" value="true"/> + <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> + <param name="out_type" value="qcML"/> + <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/> + </test> + <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input --> + <param name="adv_opts|test" value="true"/> + <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> + <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/> + <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/> + <param name="out_type" value="qcML"/> + <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/> + </test> + <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input --> + <param name="adv_opts|test" value="true"/> + <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/> + <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/> + <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/> + <param name="out_type" value="qcML"/> + <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/> + </test> +</tests> <help><![CDATA[Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_QCCalculator.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCCalculator.html]]></help> <expand macro="references"/> </tool>