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author | workflow4metabolomics |
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date | Fri, 05 Aug 2022 17:25:45 +0000 |
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<tool id="ms2snoop" name="MS2 Snoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" > <description> MS1/MS2 spectra and associated adducts extraction and cleaning </description> <macros> <import>macros.xml</import> </macros> <edam_topics> <edam_topic>topic_0091</edam_topic> <edam_topic>topic_3370</edam_topic> </edam_topics> <edam_operations> <edam_operation>operation_3803</edam_operation> <edam_operation>operation_3860</edam_operation> </edam_operations> <requirements> <requirement type="package" version="4.1.3">r-base</requirement> <requirement type="package" version="1.7.1">r-optparse</requirement> <requirement type="package" version="4.9.15">sirius-csifingerid</requirement> <requirement type="package" version="3.0">zip</requirement> </requirements> <stdio> <exit_code range="1" level="fatal" description="Missing parameter error" /> <exit_code range="2" level="fatal" description="Bad parameter's value" /> <exit_code range="3" level="fatal" description="Missing input file" /> <exit_code range="4:254" level="fatal" description="Unknown error" /> <exit_code range="255" level="fatal" description="No any result to output" /> <regex match="Error in\s+.*:\s+.*" /> </stdio> <version_command> Rscript '$__tool_directory__/MS2snoop.R' --version | head -n 1 </version_command> <command> <![CDATA[ Rscript '$__tool_directory__/MS2snoop.R' --output '$frag_result_txt' --compounds '$compound_txt' --fragments '$peaklist_frag_tsv' --precursors '$peaklist_preco_tsv' --tolmz '$tolmz' --tolrt '$tolrt' --seuil_ra '$seuil_ra' --mzdecimal '$mzdecimal' --r_threshold '$r_threshold' --min_number_scan '$min_number_scan' --ionization '$sirius.ionization' --fragment_match_delta '$sirius.fragment_match_delta' --fragment_match_delta_unit '$sirius.fragment_match_delta_unit' $advenced.pdf $advenced.debug $advenced.verbose ]]> </command> <inputs> <param argument="--compound_txt" type="data" format="tabular,csv,tsv" label="list of compounds" help=" The table must fit the format: compound_name [MANDATORY] ; inchikey [MANDATORY] ; elemcomposition [OPTIONAL] ; mz [MANDATORY] ; rtsec [MANDATORY]. " /> <param argument="--peaklist_frag_tsv" type="data" format="tabular,csv,tsv" label="MSpurity fragments file" /> <param argument="--peaklist_preco_tsv" type="data" format="tabular,csv,tsv" label="MSpurity precursors file" /> <param argument="--tolmz" type="float" min="0.0001" max="10" value="0.01" label="MZ Tolerence" help="M/z tolerance to determine if a precursor matches a compound" /> <param argument="--tolrt" type="integer" min="0" max="30" value="20" label="RT Tolerence (in seconds)" help=" Retention time tolerance to determine if a precursor matches a compound " /> <param argument="--seuil_ra" type="float" min="0" max="1" value="0.05" label="R-Pearson correlation threshold used to filter fragments" /> <param argument="--mzdecimal" type="integer" min="0" max="5" value="0" label="Number of decimal to output M/z values with" /> <param argument="--r_threshold" type="float" min="0" value="0.85" label=" Minimun correlation with absolute intensity value to reach for a fragment to be considered as valid. In PDF generation, invalid fragments will be displayed in grey. " /> <param argument="--min_number_scan" type="integer" min="0" max="25" value="8" label="Present in at least X scan" help=" Mininum scan number in which a fragment must be found, to be kept. " /> <section title="Sirius Parameters" name="sirius"> <param argument="--ionization" type="select" label="Which ionization" help="Select the ionization to use in sirius" optional="true" > <option value="[M+H]+" selected="true">[M+H]+</option> <option value="[M-H]-">[M-H]-</option> <option value="[M+?]+">[M+?]+</option> <option value="[M+K]+">[M+K]+</option> <option value="[M+Na]+">[M+Na]+</option> <option value="[M+H-H2O]+">[M+H-H2O]+</option> <option value="[M+H-H4O2]+">[M+H-H4O2]+</option> <option value="[M+NH4]+">[M+NH4]+</option> <option value="[M+Cl]-">[M+Cl]-</option> <option value="[M-H2O-H]-">[M-H2O-H]-</option> <option value="[M+Br]-">[M+Br]-</option> </param> <param argument="--fragment_match_delta" type="float" min="0" max="25" value="10" label="Fragment match delta" help=" Delta that determines if a fragment found by sirius is linked to a certain M/z value. Zero means all fragments found by sirius will be associated even when M/z difference is aberant. " /> <param argument="--fragment_match_delta_unit" type="select" label="Delta unit" help="Select the unit of the fragment match delta" optional="true" > <option value="ppm" selected="true">PPM</option> <option value="mz">M/z</option> </param> </section> <section title="Advenced Options" name="advenced"> <param argument="--pdf" type="boolean" value="" optional="true" label="Output PDF" help="The tool will output some pdf in a zip file" truevalue="--pdf_path '$pdf_output'" falsevalue="" /> <param argument="--verbose" type="boolean" value="" optional="true" label="Verbose logs" help="The tool will print more logs" truevalue="--verbose" falsevalue="" /> <param argument="--debug" type="boolean" value="" optional="true" label="Debug statements" help="The tool will print debug statements" truevalue="--debug" falsevalue="" /> </section> </inputs> <outputs> <data name="frag_result_txt" format="tsv" label="${tool.name} on ${peaklist_frag_tsv.name}" /> <data name="pdf_output" format="zip" label="${tool.name} PDFs for ${peaklist_frag_tsv.name}" > <filter>advenced['pdf']</filter> </data> </outputs> <tests> <test> <!-- Regular test with no option --> <param name="compound_txt" value="compounds_pos.txt" /> <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> <output name="frag_result_txt" file="compound_fragments_result.txt" /> <assert_stdout> <expand macro="has_regular_stdout"/> <expand macro="has_not_verbose_stdout"/> <expand macro="has_not_debug_stdout"/> </assert_stdout> </test> <test> <!-- Regular files with verbose output --> <param name="compound_txt" value="compounds_pos.txt" /> <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> <param name="verbose" value="--verbose" /> <output name="frag_result_txt" file="compound_fragments_result.txt" /> <assert_stdout> <expand macro="has_regular_stdout"/> <expand macro="has_verbose_stdout"/> <expand macro="has_not_debug_stdout"/> </assert_stdout> </test> <test> <!-- Regular test with debug outputs --> <param name="compound_txt" value="compounds_pos.txt" /> <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> <param name="debug" value="--debug" /> <output name="frag_result_txt" file="compound_fragments_result.txt" /> <assert_stdout> <expand macro="has_smol_stdout"/> <expand macro="has_debug_stdout"/> <expand macro="has_not_verbose_stdout"/> </assert_stdout> </test> <test> <!-- Regular test with both verbose and debug outputs --> <param name="compound_txt" value="compounds_pos.txt" /> <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> <param name="debug" value="--debug" /> <param name="verbose" value="--verbose" /> <output name="frag_result_txt" file="compound_fragments_result.txt" /> <assert_stdout> <expand macro="has_smol_stdout"/> <expand macro="has_debug_stdout"/> <expand macro="has_smol_verbose_stdout"/> </assert_stdout> </test> <test> <!-- This test mixes tsv, csv, and so, and ms2snoop is expected handle them like usual. --> <param name="compound_txt" value="compounds_pos.csv" /> <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> <param name="verbose" value="--verbose" /> <output name="frag_result_txt" file="compound_fragments_result.txt" /> <assert_stdout> <expand macro="has_regular_stdout"/> <expand macro="has_verbose_stdout"/> <expand macro="has_not_debug_stdout"/> </assert_stdout> </test> <test> <!-- This test contains smaller datasets. This is the "regular" smol test, to prepare further smolah tests. --> <param name="ionization" value="[M+?]+" /> <param name="mzdecimal" value="3" /> <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" /> <output name="frag_result_txt" file="smol/out-smol-base.tsv" /> </test> <test> <!-- Test for pdf generation --> <param name="pdf" value="True" /> <param name="ionization" value="[M+?]+" /> <param name="mzdecimal" value="3" /> <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" /> <output name="frag_result_txt" file="smol/out-smol-base.tsv" /> </test> <test> <!-- test for delta in ppm --> <param name="ionization" value="[M+?]+" /> <param name="mzdecimal" value="3" /> <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" /> <param name="fragment_match_delta" value="8.542" /> <output name="frag_result_txt" file="smol/out-smol-delta-8.542.tsv" /> </test> <test> <!-- test for delta in m/z --> <param name="ionization" value="[M+?]+" /> <param name="mzdecimal" value="3" /> <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" /> <param name="fragment_match_delta" value="0.05" /> <param name="fragment_match_delta_unit" value="mz" /> <output name="frag_result_txt" file="smol/out-smol-delta-0.05mz.tsv" /> </test> <!-- === expected to fail tests === --> <test expect_exit_code="2" expect_failure="true"> <!-- This test uses old format for molecules file. Is is expected to fail --> <param name="compound_txt" value="compounds_pos_old_format.txt" /> <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> <assert_stderr> <has_line line="Error: Some columns are missing: compound_name, rtsec, inchikey" /> </assert_stderr> </test> </tests> <help><![CDATA[ @AUTHORS@ ============== MS2 validation ============== ----------- Description ----------- MS2snoop use results of msPurity to find spectra of standards listed in a compounds file. Check the fragments and precursor using correlation of among the different scans of fragments ----------------- Workflow position ----------------- -------------- Upstream tools -------------- +-------------------------+-----------------+--------+------------+ | Name | output file | format | parameter | +=========================+=================+========+============+ | msPurity.purityA | NA | TSV | NA | +-------------------------+-----------------+--------+------------+ | msPurity.frag4feature | NA | TSV | NA | +-------------------------+-----------------+--------+------------+ ---------------- Downstream tools ---------------- +-------------------------+-----------------+--------+------------+ | Name | output file | format | parameter | +=========================+=================+========+============+ | NA | NA | NA | NA | +-------------------------+-----------------+--------+------------+ ----------- Input files ----------- +----------------------------------------------+------------+ | Parameter : num + label | Format | +===========================+==================+============+ | Input from msPurity Precursor | TSV,CSV | +----------------------------------------------+------------+ | Input from msPurity fragment | TSV,CSV | | Input compounds file to search in precursor | | +----------------------------------------------+------------+ | and fragment (Name + m/z + ret Time) | TSV,CSV | +----------------------------------------------+------------+ @PARAMETERS@ @OUTPUTS@ @CHANGELOG@ ]]></help> </tool>