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metamorpheus initial commit #587
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6e86fac
metamorpheus initial commit
jj-umn 48d3dfd
Create .shed.yml
jj-umn 775042a
Add profile 21.05 for toml datatype
jj-umn 5bb772f
Merge branch 'master' into metamorpheus
bgruening 7c57a8a
Add mmsettings option
jj-umn d7af9ee
Merge branch 'metamorpheus' of https://github.com/jj-umn/tools-galaxy…
jj-umn 7a40b99
Update metamorpheus_calibration.xml
jj-umn 4c292fe
MetaMorpheus param fixes
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|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| owner: galaxyp | ||
| name: metamorpheus | ||
| categories: | ||
| - Proteomics | ||
| description: MetaMorpheus MS Search Application | ||
| long_description: | | ||
| MetaMorpheus is a bottom-up proteomics database search software | ||
| with integrated post-translational modification (PTM) discovery capability. | ||
| This application combines features of Morpheus and G-PTM-D in a single tool. | ||
|
|
||
| Features automatic inclusion of known PTMs (Post Translational Modifications) | ||
| when a UniProt Proteome is used as the search database. | ||
|
|
||
| homepage_url: https://github.com/smith-chem-wisc/MetaMorpheus | ||
| remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus | ||
| type: unrestricted |
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|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| <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 ${on_string} prose.txt" from_work_dir="output/Task1CalibrationTask/prose.txt"/> | ||
| <expand macro="calibrated_outputs"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="spectrums" ftype="mzml" value="SmallCalibratible_Yeast.mzML"/> | ||
| <param name="databases" ftype="fasta" value="SmallYeast.fasta"/> | ||
| <output name="results"> | ||
| <assert_contents> | ||
| <has_text text="MS2 calibration datapoint count:" /> | ||
| <has_text text="Engine type: CalibrationEngine" /> | ||
| </assert_contents> | ||
| </output> | ||
| <output_collection name="calibrated_scans" type="list"> | ||
| <element name="SmallCalibratible_Yeast-calib.mzML"> | ||
| <assert_contents> | ||
| <has_text_matching expression="id=.SmallCalibratible_Yeast-calib" /> | ||
| <has_text_matching expression="dataProcessing id=.mzLibProcessing" /> | ||
| </assert_contents> | ||
| </element> | ||
| </output_collection> | ||
|
|
||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| @METAMORPHEUS_HELP@ | ||
| ]]></help> | ||
| <expand macro="citations" /> | ||
| </tool> | ||
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| <tool id="metamorpheus_g_ptm_d" name="MetaMorpeus G-PTM-D" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5"> | ||
| <description>Post-translational modification (PTM) discovery</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements" /> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| @PREPARE_INPUTS@ | ||
| @LN_CALIB_TOML@ | ||
| @MERGE_TOMLS@ | ||
| metamorpheus | ||
| -t tasksettings.toml | ||
| ## -s #echo ' '.join($spectrum_names)# | ||
| -s $inputs_dir | ||
| -d #echo ' '.join($database_names)# | ||
| -o output | ||
| --mmsettings data | ||
| ]]></command> | ||
| <configfiles> | ||
| <configfile name="default_toml"><![CDATA[#slurp | ||
| @DEFAULT_GPTMD_TOML@ | ||
| ]]></configfile> | ||
| <configfile name="user_toml"> | ||
| @GPTMD_CONFIG@ | ||
| @COMMON_CONFIG@ | ||
| </configfile> | ||
| <configfile name="task_settings_toml">#slurp | ||
| </configfile> | ||
| </configfiles> | ||
| <inputs> | ||
| <expand macro="input_spectrums" multiple="true" filetype="Calibrated Spectrum"/> | ||
| <expand macro="calib_toml"/> | ||
| <expand macro="input_databases"/> | ||
| <expand macro="input_toml"/> | ||
| <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 ${on_string} prose.txt" from_work_dir="output/Task*GptmdTask/prose.txt"/> | ||
| <data name="db_xml" format="uniprotxml" label="${tool.name} on ${on_string} ${databases[0].name.rsplit('.',1)[0]}GPTMD.xml" from_work_dir="output/Task*GptmdTask/*GPTMD.xml"/> | ||
| <data name="psmtsv" format="tabular" label="${tool.name} on ${on_string} GPTMD_Candidates.psmtsv" from_work_dir="output/Task*GptmdTask/GPTMD_Candidates.psmtsv"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="spectrums" ftype="mzml" value="SmallCalibratible_Yeast-calib.mzML"/> | ||
| <param name="calib_tomls" ftype="toml" value="SmallCalibratible_Yeast-calib.toml"/> | ||
| <param name="databases" ftype="fasta" value="SmallYeast_uniprot.xml"/> | ||
| <output name="results"> | ||
| <assert_contents> | ||
| <has_text text="Engine type: GptmdEngine" /> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="db_xml"> | ||
| <assert_contents> | ||
| <has_text text="mzLibProteinDb" /> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| @METAMORPHEUS_HELP@ | ||
| ]]></help> | ||
| <expand macro="citations" /> | ||
| </tool> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| <tool id="metamorpheus_search" name="MetaMorpeus Database Search" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5"> | ||
| <description>identify peptides by their fragmentation spectra</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements" /> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| @PREPARE_INPUTS@ | ||
| @LN_CALIB_TOML@ | ||
| @MERGE_TOMLS@ | ||
| metamorpheus | ||
| -t tasksettings.toml | ||
| -s ${inputs_dir} | ||
| -d #echo ' '.join($database_names)# | ||
| -o output | ||
| --mmsettings data | ||
| ]]></command> | ||
| <configfiles> | ||
| <configfile name="default_toml"><![CDATA[#slurp | ||
| @DEFAULT_SEARCH_TOML@ | ||
| ]]></configfile> | ||
| <configfile name="user_toml"> | ||
| @SEARCH_CONFIG@ | ||
| @COMMON_CONFIG@ | ||
| </configfile> | ||
| <configfile name="task_settings_toml">#slurp | ||
| </configfile> | ||
| </configfiles> | ||
| <inputs> | ||
| <expand macro="input_spectrums" multiple="true" filetype="Calibrated Spectrum"/> | ||
| <expand macro="calib_toml"/> | ||
| <expand macro="input_databases"/> | ||
| <expand macro="input_toml"/> | ||
| <expand macro="common_params"/> | ||
| <expand macro="search_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 ${on_string} prose.txt" from_work_dir="output/Task*SearchTask/prose.txt"/> | ||
| <data name="allpsms" format="tabular" label="${tool.name} on ${on_string} AllPSMs.psmtsv" from_work_dir="output/Task*SearchTask/AllPSMs.psmtsv"/> | ||
| <data name="allpsms_percolator" format="tabular" label="${tool.name} on ${on_string} AllPSMs_FormattedForPercolator.tab" from_work_dir="output/Task*SearchTask/AllPSMs_FormattedForPercolator.tab"/> | ||
| <data name="allpeptides" format="tabular" label="${tool.name} on ${on_string} AllPeptides.psmtsv" from_work_dir="output/Task*SearchTask/AllPeptides.psmtsv"/> | ||
| <data name="allquantifiedpeaks" format="tabular" label="${tool.name} on ${on_string} AllQuantifiedPeaks.tsv" from_work_dir="output/Task*SearchTask/AllQuantifiedPeaks.tsv"> | ||
| </data> | ||
| <data name="allquantifiedpeptides" format="tabular" label="${tool.name} on ${on_string} AllQuantifiedPeptides.tsv" from_work_dir="output/Task*SearchTask/AllQuantifiedPeptides.tsv"> | ||
| </data> | ||
| <data name="allquantifiedprotein" format="tabular" label="${tool.name} on ${on_string} AllQuantifiedProteinGroups.tsv" from_work_dir="output/Task*SearchTask/AllQuantifiedProteinGroups.tsv"> | ||
| </data> | ||
| <expand macro="search_collection_outputs"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="spectrums" ftype="mzml" value="SmallCalibratible_Yeast-calib.mzML"/> | ||
| <param name="calib_tomls" ftype="toml" value="SmallCalibratible_Yeast-calib.toml"/> | ||
| <param name="databases" ftype="fasta" value="SmallYeastGPTMD.xml"/> | ||
| <output name="results"> | ||
| <assert_contents> | ||
| <has_text text="Engine type: ProteinScoringAndFdrEngine" /> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="allpsms"> | ||
| <assert_contents> | ||
| <has_text text="KGNNTANATN[Common Artifact:Deamidation on N]SANTVQK" /> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| @METAMORPHEUS_HELP@ | ||
| ]]></help> | ||
| <expand macro="citations" /> | ||
| </tool> |
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8,122 changes: 8,122 additions & 0 deletions
8,122
tools/metamorpheus/test-data/SmallCalibratible_Yeast-calib.mzML
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tools/metamorpheus/test-data/SmallCalibratible_Yeast-calib.toml
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,2 @@ | ||
| PrecursorMassTolerance = "±3.7699 PPM" | ||
| ProductMassTolerance = "±8.4670 PPM" |
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can you add
expect_num_outputs.. which is always a good idea if there are outputs with filters.