Mercurial > repos > galaxyp > metamorpheus
view metamorpheus_calibration.xml @ 1:975f857ad9b8 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0"
author | galaxyp |
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date | Wed, 26 May 2021 16:10:35 +0000 |
parents | e8d7b7dc55fc |
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<tool id="metamorpheus_calibration" name="MetaMorpeus Calibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5"> <description>identify peptides by their calibrate the m/z values of all peaks in the spectra</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @PREPARE_INPUTS@ @MERGE_TOMLS@ metamorpheus -t tasksettings.toml ## -s #echo ' '.join($spectrum_names)# -s $inputs_dir -d #echo ' '.join($database_names)# -o output --mmsettings data ]]></command> <configfiles> <configfile name="default_toml"><![CDATA[#slurp @DEFAULT_CALIBRATION_TOML@ ]]></configfile> <configfile name="user_toml"> @CALIBRATE_CONFIG@ @COMMON_CONFIG@ </configfile> <configfile name="task_settings_toml">#slurp </configfile> </configfiles> <inputs> <expand macro="input_spectrums" multiple="true"/> <expand macro="input_databases"/> <expand macro="input_toml"/> <expand macro="calibrate_params"/> <expand macro="common_params"/> </inputs> <outputs> <expand macro="output_settings_toml"/> <data name="results" format="txt" label="${tool.name} on ${on_string} results.txt" from_work_dir="output/allresults.txt"/> <data name="prose" format="txt" label="${tool.name} on ${on_string} prose.txt" from_work_dir="output/Task1CalibrationTask/prose.txt"/> <expand macro="calibrated_outputs"/> </outputs> <tests> <test> <param name="spectrums" ftype="mzml" value="SmallCalibratible_Yeast.mzML"/> <param name="databases" ftype="fasta" value="SmallYeast.fasta"/> <output name="results"> <assert_contents> <has_text text="MS2 calibration datapoint count:" /> <has_text text="Engine type: CalibrationEngine" /> </assert_contents> </output> <output_collection name="calibrated_scans" type="list"> <element name="SmallCalibratible_Yeast-calib.mzML"> <assert_contents> <has_text_matching expression="id=.SmallCalibratible_Yeast-calib" /> <has_text_matching expression="dataProcessing id=.mzLibProcessing" /> </assert_contents> </element> </output_collection> </test> </tests> <help><![CDATA[ @METAMORPHEUS_HELP@ ]]></help> <expand macro="citations" /> </tool>