Mercurial > repos > galaxyp > openms_openswathassaygenerator
diff OpenSwathAssayGenerator.xml @ 14:74d39f98b0c4 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:41:12 +0000 |
| parents | de7a553552a6 |
| children |
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--- a/OpenSwathAssayGenerator.xml Thu Dec 01 19:07:50 2022 +0000 +++ b/OpenSwathAssayGenerator.xml Fri Jun 14 21:41:12 2024 +0000 @@ -1,6 +1,5 @@ -<?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]--> +<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]--> <tool id="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Generates assays according to different models for a specific TraML</description> <macros> @@ -15,15 +14,15 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $swath_windows_file: mkdir swath_windows_file && - ln -s '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' && + cp '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' && #end if #if $unimod_file: mkdir unimod_file && - ln -s '$unimod_file' 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)' && + cp '$unimod_file' 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)' && #end if ## Main program call @@ -55,40 +54,41 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" 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=""> + <param argument="-in" type="data" format="mrm,pqp,tabular,traml" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/> + <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help=""> <option value="TraML">traml</option> <option value="pqp">pqp</option> <option value="tsv">tabular (tsv)</option> + <validator type="expression" message="A value needs to be selected">value != "select a value"</validator> <expand macro="list_string_san" name="out_type"/> </param> - <param argument="-min_transitions" type="integer" optional="true" value="6" label="minimal number of transitions" help=""/> - <param argument="-max_transitions" type="integer" optional="true" value="6" label="maximal number of transitions" help=""/> - <param argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help=""> + <param argument="-min_transitions" type="integer" value="6" label="minimal number of transitions" help=""/> + <param argument="-max_transitions" type="integer" value="6" label="maximal number of transitions" help=""/> + <param argument="-allowed_fragment_types" type="text" value="b,y" label="allowed fragment types" help=""> <expand macro="list_string_san" name="allowed_fragment_types"/> </param> - <param argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help=""> + <param argument="-allowed_fragment_charges" type="text" value="1,2,3,4" label="allowed fragment charge states" help=""> <expand macro="list_string_san" name="allowed_fragment_charges"/> </param> <param argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/> <param argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/> - <param argument="-precursor_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/> - <param argument="-precursor_lower_mz_limit" type="float" optional="true" value="400.0" label="lower MZ limit for precursor ions" help=""/> - <param argument="-precursor_upper_mz_limit" type="float" optional="true" value="1200.0" label="upper MZ limit for precursor ions" help=""/> - <param argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/> - <param argument="-product_lower_mz_limit" type="float" optional="true" value="350.0" label="lower MZ limit for fragment ions" help=""/> - <param argument="-product_upper_mz_limit" type="float" optional="true" value="2000.0" label="upper MZ limit for fragment ions" help=""/> + <param argument="-precursor_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/> + <param argument="-precursor_lower_mz_limit" type="float" value="400.0" label="lower MZ limit for precursor ions" help=""/> + <param argument="-precursor_upper_mz_limit" type="float" value="1200.0" label="upper MZ limit for precursor ions" help=""/> + <param argument="-product_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/> + <param argument="-product_lower_mz_limit" type="float" value="350.0" label="lower MZ limit for fragment ions" help=""/> + <param argument="-product_upper_mz_limit" type="float" value="2000.0" label="upper MZ limit for fragment ions" help=""/> <param argument="-swath_windows_file" type="data" format="txt" optional="true" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline" help="Note that the first line is a header and will be skipped select txt data sets(s)"/> <param argument="-unimod_file" type="data" format="xml" optional="true" label="(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability" help=" select xml data sets(s)"/> <param argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions should be generated for IPF" help="Note: Requires setting 'unimod_file'"/> <expand macro="adv_opts_macro"> - <param argument="-max_num_alternative_localizations" type="integer" optional="true" value="10000" label="IPF: maximum number of site-localization permutations" help=""/> + <param argument="-max_num_alternative_localizations" type="integer" value="10000" label="IPF: maximum number of site-localization permutations" help=""/> <param argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/> <param argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/> <param argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/> <param argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/> <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=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -107,7 +107,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_OpenSwathAssayGenerator_test_1 --> + <tests> + <!-- TOPP_OpenSwathAssayGenerator_test_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="max_num_alternative_localizations" value="10000"/> @@ -119,7 +120,7 @@ <param name="test" value="true"/> </section> <param name="in" value="OpenSwathAssayGenerator_input.TraML"/> - <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <output name="out" value="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <param name="min_transitions" value="6"/> <param name="max_transitions" value="6"/> @@ -140,6 +141,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_OpenSwathAssayGenerator_test_2 --> <test expect_num_outputs="2"> @@ -153,7 +157,7 @@ <param name="test" value="true"/> </section> <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> - <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <output name="out" value="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <param name="min_transitions" value="6"/> <param name="max_transitions" value="6"/> @@ -175,6 +179,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_OpenSwathAssayGenerator_test_3 --> <test expect_num_outputs="2"> @@ -188,7 +195,7 @@ <param name="test" value="true"/> </section> <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> - <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> + <output name="out" value="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> <param name="out_type" value="TraML"/> <param name="min_transitions" value="6"/> <param name="max_transitions" value="6"/> @@ -210,11 +217,14 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> </tests> <help><![CDATA[Generates assays according to different models for a specific TraML -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathAssayGenerator.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathAssayGenerator.html]]></help> <expand macro="references"/> </tool>