Mercurial > repos > galaxyp > fragpipe
diff macros.xml @ 7:b4f6df8fa89b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
| author | galaxyp |
|---|---|
| date | Wed, 01 Oct 2025 22:20:54 +0000 |
| parents | 59fec1e2a6c3 |
| children |
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--- a/macros.xml Sun Mar 30 23:00:45 2025 +0000 +++ b/macros.xml Wed Oct 01 22:20:54 2025 +0000 @@ -1,7 +1,15 @@ <macros> <import>msfragger_macros.xml</import> - <token name="@TOOL_VERSION@">20.0</token> - <token name="@VERSION_SUFFIX@">6</token> + <token name="@TOOL_VERSION@">23.0</token> + <token name="@VERSION_SUFFIX@">0</token> + + <!-- + These keys were generated ONLY for use by the Galaxy tool wrapper, and only after + the user has selected agreed to the academic-use only terms in the tool wrapper. + --> + <token name="@MSFRAGGER_ACADEMIC_USE_KEY@">f28c4be2-759b0a11-6c1ea652-1240565a</token> + <token name="@IONQUANT_ACADEMIC_USE_KEY@">b6c0ad83-9a4e8900-3e83d29c-aeba3bfb</token> + <token name="@DIATRACER_ACADEMIC_USE_KEY@">8de4daf3-a090ed0d-0acdb00a-1485d8a7</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement> @@ -59,7 +67,14 @@ #for $sf in $inputs #set $i_name = $ln_name($sf) - ln -s '$sf' 'scans/${i_name}' && + + ## speclib library does not follow links + #if $wf.workflow_name == "DIA_SpecLib_Quant" + cp '$sf' 'scans/${i_name}' && + #else + ln -s '$sf' 'scans/${i_name}' && + #end if + #end for ]]></token> @@ -117,7 +132,12 @@ awk 'NR==1{printf("Experiment\t%s\n",\$0);}' \$i > concat_\${f}; fi; awk 'NR>1{printf("'"\${d}"'\t%s\n",\$0);}' \$i >> concat_\${f}; t=\$(echo \${i} | tr '/' '.'); - mv \${i} \${t}; n=\$((n+1)); + if [[ \${i} == \${t} ]]; then + mv \${i} 1.\${i}; + else + mv \${i} \${t}; + fi; + n=\$((n+1)); done; done ]]></token> @@ -151,16 +171,17 @@ --> <xml name="workflow"> <conditional name="wf"> - <param name="workflow_name" type="select" label="Workflow" help="Note: MSBooster is currently disabled in all Galaxy FragPipe workflows."> - <option value="Default">Default</option> + <param name="workflow_name" type="select" label="Workflow"> + <option value="Basic-Search">Basic-Search</option> <option value="Open">Open</option> <option value="Nonspecific-HLA">Nonspecific-HLA</option> <option value="LFQ-MBR">LFQ-MBR</option> <option value="TMT10">TMT10</option> <option value="TMT11">TMT11</option> + <option value="DIA_SpecLib_Quant">DIA_SpecLib_Quant</option> </param> - <when value="Default"> + <when value="Basic-Search"> <section name="msfragger" expanded="false" title="MSFragger Options"> <expand macro="msfragger_default"/> </section> @@ -180,6 +201,8 @@ <expand macro="label_free_quantification" yes="false" no="true"/> <expand macro="ptm_shepherd" yes="false" no="true" c="true" z="true"/> <expand macro="isobaric_quantification" yes="false" no="true"/> + <expand macro="diann_quantification" yes="false" no="true"/> + <expand macro="dia_pseuedo_ms2"/> </when> <when value="Open"> @@ -204,6 +227,8 @@ <expand macro="label_free_quantification" yes="false" no="true"/> <expand macro="ptm_shepherd" yes="true" no="false"/> <expand macro="isobaric_quantification" yes="false" no="true" bridge="false" pool="true"/> + <expand macro="diann_quantification" yes="false" no="true"/> + <expand macro="dia_pseuedo_ms2"/> </when> <when value="Nonspecific-HLA"> @@ -226,6 +251,8 @@ <expand macro="label_free_quantification" yes="false" no="true"/> <expand macro="ptm_shepherd" yes="false" no="true"/> <expand macro="isobaric_quantification" yes="false" no="true"/> + <expand macro="diann_quantification" yes="false" no="true"/> + <expand macro="dia_pseuedo_ms2"/> </when> <when value="LFQ-MBR"> @@ -248,6 +275,34 @@ <expand macro="label_free_quantification" yes="true" no="false"/> <expand macro="ptm_shepherd" yes="false" no="true"/> <expand macro="isobaric_quantification" yes="false" no="true"/> + <expand macro="diann_quantification" yes="false" no="true"/> + <expand macro="dia_pseuedo_ms2"/> + </when> + + <when value="DIA_SpecLib_Quant"> + <section name="msfragger" expanded="false" title="MSFragger Options"> + <expand macro="msfragger_dia_speclib_quant"/> + </section> + <expand macro="validation" + pep="false" + perc="false" + boost="true" + no="false" + masswidth="5" + clevel="0" + accmass="true" + decoyprobs="true" + nonparam="true" + expectscore="true" + ppm="true" + combined_pepxml="false" + protp_minprob="0.5" + perc_minprob="0.7"/> + <expand macro="label_free_quantification" yes="false" no="true"/> + <expand macro="ptm_shepherd" yes="false" no="true" c="true" z="true"/> + <expand macro="isobaric_quantification" yes="false" no="true"/> + <expand macro="diann_quantification" yes="true" no="false"/> + <expand macro="dia_pseuedo_ms2"/> </when> <when value="TMT10"> @@ -284,6 +339,8 @@ <expand macro="isobaric_quantification" yes="true" no="false" plex="@PLEX@" level="2" ref_tag="Bridge" mod_tag="none"/> <expand macro="label_free_quantification" yes="false" no="true"/> <expand macro="ptm_shepherd" yes="false" no="true" token_unimod="false" token_common="true"/> + <expand macro="diann_quantification" yes="false" no="true"/> + <expand macro="dia_pseuedo_ms2"/> </xml> <!-- Generates the FragPipe workflow--> @@ -311,10 +368,55 @@ ## Get the MSFragger Params (shared with the MSFragger tool) #set $prefix = $wf.msfragger + @MSFRAGGER_PARAM_DICT@ #if len($vmods) > 0 - #set $msfragger_dict['table.var-mods'] = '; '.join([$re.sub('^(.*,)(\d)$','\\1True,\\2',m) for m in $vmods]) + #set $msfragger_dict['table.var-mods'] = '; '.join([$re.sub('^(.*,)(\d)$','\\1true,\\2',m) for m in $vmods]) #end if + + #set $fmod_items = [ + ("add_Cterm_peptide", "C-Term Peptide"), + ("add_Nterm_peptide", "N-Term Peptide"), + ("add_Cterm_protein", "C-Term Protein"), + ("add_Nterm_protein", "N-Term Protein"), + ("add_G_glycine","G (glycine)"), + ("add_A_alanine", "A (alanine)"), + ("add_S_serine", "S (serine)"), + ("add_P_proline", "P (proline)"), + ("add_V_valine", "V (valine)"), + ("add_T_threonine", "T (threonine)"), + ("add_C_cysteine", "C (cysteine)"), + ("add_L_leucine", "L (leucine)"), + ("add_I_isoleucine", "I (isoleucine)"), + ("add_N_asparagine", "N (asparagine)"), + ("add_D_aspartic_acid", "D (aspartic acid)"), + ("add_Q_glutamine", "Q (glutamine)"), + ("add_K_lysine", "K (lysine)"), + ("add_E_glutamic_acid", "E (glutamic acid)"), + ("add_M_methionine", "M (methionine)"), + ("add_H_histidine", "H (histidine)"), + ("add_F_phenylalanine", "F (phenylalanine)"), + ("add_R_arginine", "R (arginine)"), + ("add_Y_tyrosine", "Y (tyrosine)"), + ("add_W_tryptophan", "W (tryptophan)"), + ("add_B_user_amino_acid", "B "), + ("add_J_user_amino_acid", "J"), + ("add_O_user_amino_acid", "O"), + ("add_U_user_amino_acid", "U"), + ("add_X_user_amino_acid", "X"), + ("add_Z_user_amino_acid", "Z") + ] + #set $fmod_string = "" + #for $m in $fmod_items + #set fmod_var_name = $m[0] + #set fmod_wf_name = $m[1] + #set $fmod_bool = $fmod_bools.get($fmod_var_name + "_bool") + #set $fmod_val = $fmod_vals.get($fmod_var_name) + #set $fmod_string += "; " + ",".join([str($fmod_val),str($fmod_wf_name),str($fmod_bool),"-1"]) + #end for + #set $fmod_string = $fmod_string[2:] + #set $msfragger_dict['table.fix-mods'] = $fmod_string + #for $k in $msfragger_dict.keys() #set $kv = $k + '=' + str($msfragger_dict[$k]) #set $wfk = 'msfragger.' + $k @@ -325,6 +427,14 @@ @PTM_SHEPHERD@ @LABEL_FREE_QUANTIFICATION@ @ISOBARIC_QUANTIFICATION@ + @DIANN_QUANTIFICATION@ + @DIA_PSEUDO_MS2@ + + ## These values are specifically set by the GUI when running DIA_SpecLib_Quant + #if $wf.workflow_name == "DIA_SpecLib_Quant" + #set $wfdict["ptmshepherd.annotate_assigned_mods"] = "false" + #set $wfdict["ptmshepherd.use_msfragger_localization"] = "true" + #end if ## Populate the workflow with configuration and comment dictionary entries populated by tool params. #for $comment in $comments @@ -339,10 +449,10 @@ </xml> <!-- Percolator options --> - <xml name="percolator"> + <xml name="percolator" token_perc_minprob="0.5"> <section name="percolator" expanded="true" title="Percolator"> <param name="keep_tsv_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep intermediate files"/> - <param name="min_prob" type="float" value="0.5" label="Minimum probability (default 0.5)"/> + <param name="min_prob" type="float" value="@PERC_MINPROB@" label="Minimum probability (default 0.5)"/> </section> </xml> @@ -358,15 +468,25 @@ <section name="msbooster" expanded="true" title="MSBooster"> <param name="predict_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict RT"/> <param name="predict_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict spectra"/> - <param name="use_correlated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use correlated features"/> + <param name="predict_im" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict IM"/> + <param name="use_koina" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Koina server" help="The public server used is https://koina.wilhelmlab.org:443/v2/models"/> + <param name="find_best_rt_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find best RT model (requires Koina server)"/> + <param name="find_best_im_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find best IM model if applicable (requires Koina server)"/> + <param name="find_best_spectra_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find best spectral model (requires Koina server)"/> </section> </xml> <token name="@MSBOOSTER@"><![CDATA[ #set $prfx = $wf.validation.validation_tab.psm_validation.msbooster #set $wfdict['msbooster.run-msbooster'] = 'true' - #set $wfdict['msbooster.predict-rt'] = str($prfx.predict_rt) - #set $wfdict['msbooster.predict-spectra'] = str($prfx.predict_spectra) - #set $wfdict['msbooster.use-correlated-features'] = str($prfx.use_correlated_features) + #set $wfdict['msbooster.predict-rt'] = $prfx.predict_rt + #set $wfdict['msbooster.predict-spectra'] = $prfx.predict_spectra + #set $wfdict['msbooster.predict-im'] = $prfx.predict_im + #if $prfx.use_koina == 'true' + #set $wfdict['msbooster.koina-url'] = 'https://koina.wilhelmlab.org:443/v2/models/' + #end if + #set $wfdict['msbooster.find-best-rt-model'] = $prfx.find_best_rt_model + #set $wfdict['msbooster.find-best-spectra-model'] = $prfx.find_best_spectra_model + #set $wfdict['msbooster.find-best-im-model'] = $prfx.find_best_im_model ]]></token> @@ -379,7 +499,7 @@ </param> <when value="true"> <section name="phi_report_opts" expanded="false" title="FDR Filter and Report"> - <param name="dont_use_prot_prophet_file" type="boolean" truevalue="true" falsevalue="false" checked="false"/> + <param name="dont_use_prot_proph_file" type="boolean" truevalue="true" falsevalue="false" checked="false"/> <param name="print_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false"/> </section> </when> @@ -394,6 +514,7 @@ #set $wfdict['phi-report.run-report'] = 'true' #set $prfx = $wf.validation.validation_tab.phi_report.phi_report_opts #set $wfdict['phi-report.print-decoys'] = $prfx.print_decoys + #set $wfdict['phi-report.dont-use-prot-proph-file'] = $prfx.dont_use_prot_proph_file #else #set $wfdict['phi-report.run-report'] = 'false' #end if @@ -438,7 +559,7 @@ </xml> <!-- Protein Prophet options --> - <xml name="protein_prophet" token_minprob="0.05"> + <xml name="protein_prophet" token_protp_minprob="0.05"> <conditional name="protein_prophet"> <param name="run_protein_prophet" type="select" label="Run Protein Prophet"> <option value="true" selected="true">Yes</option> @@ -448,7 +569,7 @@ <section name="protein_prophet_opts" expanded="true" title="Protein Prophet"> <param argument="--iprophet" type="boolean" truevalue="--iprophet" falsevalue="" checked="false" label="input is from iProphet" /> <param argument="--maxppmdiff" type="integer" value="2000000" label="maximum peptide mass difference in ppm (default 2000000)" /> - <param argument="--minprob" type="float" value="@MINPROB@" label="PeptideProphet probability threshold (default 0.05)" /> + <param argument="--minprob" type="float" value="@PROTP_MINPROB@" label="PeptideProphet probability threshold (default 0.05)" /> <param argument="--nonsp" type="boolean" truevalue="--nonsp" falsevalue="" checked="false" label="do not use NSP model" /> <param argument="--subgroups" type="boolean" truevalue="--subgroups" falsevalue="" checked="false" label="do not use NOGROUPS" /> <param argument="--unmapped" type="boolean" truevalue="--unmapped" falsevalue="" checked="false" label="report results for UNMAPPED proteins" /> @@ -462,19 +583,19 @@ <token name="@PROTEINPROPHET@"><![CDATA[ #set $prfx = $wf.validation.validation_tab.protein_prophet #if $prfx.run_protein_prophet == 'true' - #set $prfx = $wf.validation.validation_tab.protein_prophet.protein_prophet_opts + #set $prfx = $wf.validation.validation_tab.protein_prophet.protein_prophet_opts #set $wfdict['protein-prophet.run-protein-prophet'] = 'true' #set $cmd_opts = [str($prfx.iprophet),str($prfx.nonsp),str($prfx.subgroups),str($prfx.unmapped)] #silent $cmd_opts.append('--maxppmdiff ' + str($prfx.maxppmdiff)) #silent $cmd_opts.append('--minprob ' + str($prfx.minprob)) #set $wfdict['protein-prophet.cmd-opts'] = ' '.join($cmd_opts).strip() #else - #set $wfdict[protein-prophet.run-protein-prophet] = 'false' + #set $wfdict['protein-prophet.run-protein-prophet'] = 'false' #end if ]]></token> <!-- Validation options. Includes PeptideProphet, Percolator, MSBooster, ProteinProphet, and CrystalC --> - <xml name="validation" token_expand="false" token_pep="false" token_perc="false" token_boost="false" token_no="true" token_masswidth="5" token_clevel="0" token_accmass="true" token_decoyprobs="true" token_nonparam="true" token_expectscore="true" token_ppm="true" token_combined_pepxml="false" token_protp_minprob="0.05"> + <xml name="validation" token_expand="false" token_pep="false" token_perc="false" token_boost="false" token_no="true" token_masswidth="5" token_clevel="0" token_accmass="true" token_decoyprobs="true" token_nonparam="true" token_expectscore="true" token_ppm="true" token_combined_pepxml="false" token_protp_minprob="0.05" token_perc_minprob="0.5"> <section name="validation" expanded="@EXPAND@" title="Validation"> <conditional name="validation_tab"> <param name="run_validation" type="select" label="Run Validation"> @@ -494,16 +615,16 @@ <expand macro="peptide_prophet" masswidth="@MASSWIDTH@" clevel="@CLEVEL@" accmass="@ACCMASS@" decoyprobs="@DECOYPROBS@" nonparam="@NONPARAM@" expectscore="@EXPECTSCORE@" ppm="@PPM@" combined_pepxml="@COMBINED_PEPXML@"/> </when> <when value="percolator"> - <expand macro="percolator"/> + <expand macro="percolator" perc_minprob="@PERC_MINPROB@"/> </when> <when value="msbooster_percolator"> <expand macro="msbooster"/> - <expand macro="percolator"/> + <expand macro="percolator" perc_minprob="@PERC_MINPROB@"/> </when> <when value="no"> </when> </conditional> - <expand macro="protein_prophet" minprob="@PROTP_MINPROB@"/> + <expand macro="protein_prophet" protp_minprob="@PROTP_MINPROB@"/> <expand macro="phi_report"/> </when> <when value="false"> @@ -514,25 +635,34 @@ <!-- Set validation workflow options --> <token name="@VALIDATION@"><![CDATA[ - #set $prfx = $wf.validation.validation_tab.psm_validation - #if $prfx.run_psm_validation == 'peptide_prophet' - #set $wfdict['run-psm-validation'] = 'true' - #set $wfdict['msbooster.run-msbooster'] = 'false' - #set $wfdict['percolator.run-percolator'] = 'false' - @PEPTIDEPROPHET@ - #elif $prfx.run_psm_validation == 'percolator' - #set $wfdict['run-psm-validation'] = 'true' + #if $wf.validation.validation_tab.run_validation == "true" + #set $prfx = $wf.validation.validation_tab.psm_validation + #if $prfx.run_psm_validation == 'peptide_prophet' + #set $wfdict['run-psm-validation'] = 'true' + #set $wfdict['msbooster.run-msbooster'] = 'false' + #set $wfdict['percolator.run-percolator'] = 'false' + @PEPTIDEPROPHET@ + #elif $prfx.run_psm_validation == 'percolator' + #set $wfdict['run-psm-validation'] = 'true' + #set $wfdict['msbooster.run-msbooster'] = 'false' + #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false' + @PERCOLATOR@ + #elif $prfx.run_psm_validation == 'msbooster_percolator' + #set $wfdict['run-psm-validation'] = 'true' + #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false' + @MSBOOSTER@ + @PERCOLATOR@ + #end if + @PROTEINPROPHET@ + @PHIREPORT@ + #else + #set $wfdict['run-psm-validation'] = 'false' #set $wfdict['msbooster.run-msbooster'] = 'false' #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false' - @PERCOLATOR@ - #elif $prfx.run_psm_validation == 'msbooster_percolator' - #set $wfdict['run-psm-validation'] = 'true' - #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false' - @MSBOOSTER@ - @PERCOLATOR@ + #set $wfdict['percolator.run-percolator'] = 'false' + #set $wfdict['protein-prophet.run-protein-prophet'] = 'false' + #set $wfdict['phi-report.run-report'] = 'false' #end if - @PROTEINPROPHET@ - @PHIREPORT@ ]]></token> <!-- PTM-Sheperd options --> @@ -597,7 +727,6 @@ <option value="z" selected="@Z@">z</option> </param> <param name="spectra_maxfragcharge" type="integer" value="" min="0" optional="true" label="Max fragment charge" help="ptmshepherd.spectra_maxfragcharge"/> - <param name="localization_background" type="integer" value="" min="0" optional="true" label="Localization background" help="ptmshepherd.localization_background"/> <param name="localization_allowed_res" type="select" label="Restrict localization to" help="ptmshepherd.localization_allowed_res"> <option value="" selected="true">none</option> <option value="all">all</option> @@ -628,14 +757,14 @@ #set $wfdict['ptmshepherd.histo_smoothbins'] = $cxt.histo_smoothbins #end if #if $cxt.precursor_tol != '' - #set $wfdict['ptmshepherd.precursor_mass_units'] = $ctx.precursor_mass_units + #set $wfdict['ptmshepherd.precursor_mass_units'] = $cxt.precursor_mass_units #set $wfdict['ptmshepherd.precursor_tol'] = $cxt.precursor_tol #end if #if $cxt.peakpicking_promRatio != '' #set $wfdict['ptmshepherd.peakpicking_promRatio'] = $cxt.peakpicking_promRatio #end if #if $cxt.peakpicking_width != '' - #set $wfdict['ptmshepherd.peakpicking_mass_units'] = $ctx.peakpicking_mass_units + #set $wfdict['ptmshepherd.peakpicking_mass_units'] = $cxt.peakpicking_mass_units #set $wfdict['ptmshepherd.peakpicking_width'] = $cxt.peakpicking_width #end if #if $cxt.peakpicking_minPsm != '' @@ -696,9 +825,6 @@ #if $cxt.spectra_maxfragcharge != '' #set $wfdict['ptmshepherd.spectra_maxfragcharge'] = $cxt.spectra_maxfragcharge #end if - #if $cxt.localization_background != '' - #set $wfdict['ptmshepherd.localization_background'] = $cxt.localization_background - #end if #set $wfdict['ptmshepherd.localization_allowed_res'] = $cxt.localization_allowed_res #else #set $wfdict['ptmshepherd.run-shepherd'] = 'false' @@ -715,10 +841,94 @@ <param name="label_free_quantification_run" type="select" label="Perform Label-Free Quantification"> <option value="default" selected="true">Use workflow default</option> <option value="no">No Label-Free Quantification</option> + <option value="ionquant">Run IonQuant</option> <option value="freequant">Run FreeQuant</option> </param> <when value="default"/> <when value="no"/> + <when value="ionquant"> + <section name="ionquant" expanded="false" title="IonQuant Label-Free Quantification"> + <param name="mbr_select" type="select" optional="true" label="Match between runs (MBR)" help="ionquant.mbr"> + <option value="0">No</option> + <option value="1">Yes</option> + </param> + <param name="normalization" type="select" optional="true" label="Normalize" help="ionquant.normalization"> + <option value="0">No</option> + <option value="1">Yes</option> + </param> + <section name="feature_detection" expanded="false" title="Feature detection"> + <param name="mztol" type="integer" value="" optional="true" label="m/z tolerance in ppm" help="ionquant.mztol (default 10)"/> + <param name="rttol" type="float" value="" optional="true" label="RT tolerance (minutes)" help="ionquant.rttol (default 0.4)"/> + <param name="imtol" type="float" value="" optional="true" label="IM tolerance (1/k0)" help="ionquant.imtol (default 0.05)"/> + </section> + <section name="mbr" expanded="false" title="Match between runs (MBR)"> + <param name="mbrrttol" type="float" value="" optional="true" label="MBR RT tolerance (minutes)" help="ionquant.mbrrttol"/> + <param name="mbrimtol" type="float" value="" optional="true" label="MBR IM tolerance (1/k0)" help="ionquant.mbrimtol"/> + <param name="mbrmincorr" type="float" value="" optional="true" label="MBR min correlation" help="ionquant.mbrmincorr"/> + <param name="mbrtoprun" type="integer" value="" optional="true" label="MBR top runs" help="ionquant.mbrtoprun"/> + <param name="ionfdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR ion FDR" help="ionquant.ionfdr"/> + <param name="peptidefdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR peptide FDR" help="ionquant.peptidefdr"/> + <param name="proteinfdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR protein FDR" help="ionquant.proteinfdr"/> + </section> + <section name="topn" expanded="false" title="Top-N options"> + <param name="tp" type="integer" value="" min="0" optional="true" label="Top N ions" help="ionquant.tp"/> + <param name="minfreq" type="float" value="" min="0.0" max="1.0" optional="true" label="Min freq" help="ionquant.minfreq"/> + </section> + <conditional name="labeling_conditional"> + <param name="labeling_option" type="select" label="Labeling option"> + <option value="lfq" selected="true">LFQ</option> + <option value="labeling">Labeling</option> + </param> + <when value="lfq"> + <section name="lfq" expanded="false" title="LFQ"> + <param name="maxlfq" type="select" optional="true" label="MaxLFQ" help="ionquant.maxlfq"> + <option value="0">No</option> + <option value="1">Yes</option> + </param> + <param name="minions" type="integer" value="" optional="true" label="Min ions" help="ionquant.minions"/> + </section> + </when> + <when value="labeling"> + <section name="labeling" expanded="false" title="Labeling-based quant"> + <param name="light" type="select" label="Light" help="ionquant.light"> + <option value="" selected="true">none</option> + <option value="C463.2366">C463.2366</option> + <option value="C464.28596">C464.28596</option> + <option value="C561.3387">C561.3387</option> + <option value="K0;R0">K0;R0</option> + </param> + <param name="medium" type="select" label="Medium" help="ionquant.medium"> + <option value="" selected="true">none</option> + <option value="K4.025107;R6.020129">K4.025107;R6.020129</option> + </param> + <param name="heavy" type="select" label="Heavy" help="ionquant.heavy"> + <option value="" selected="true">none</option> + <option value="C467.2529">C467.2529</option> + <option value="C470.29977">C470.29977</option> + <option value="C567.3462">C567.3462</option> + <option value="K8.014199;R10.008269">K8.014199;R10.008269</option> + </param> + <param name="requantify" type="select" label="Re-quantify" help="ionquant.requantify"> + <option value="0">No</option> + <option value="1" selected="true">Yes</option> + </param> + </section> + </when> + </conditional> + <section name="advanced" expanded="false" title="Advanced options"> + <param name="excludemods" type="text" optional="true" label="excludemods" help="ionquant.excludemods"> + <validator type="regex">^\s*@RE_EXCLUDEMODS@\s*$</validator> + </param> + <param name="minscans" type="integer" value="" min="0" optional="true" label="Min scans" help="ionquant.minscans"/> + <param name="minisotopes" type="integer" value="" min="1" max="3" optional="true" label="Min isotopes" help="ionquant.minisotopes"/> + <param name="locprob" type="float" value="" min="0.0" max="1.0" optional="true" label="Min site probability" help="ionquant.locprob"/> + <param name="writeindex" type="select" optional="true" label="Write index" help="ionquant.writeindex"> + <option value="0">No</option> + <option value="1">Yes</option> + </param> + </section> + </section> + </when> <when value="freequant"> <section name="freequant" expanded="false" title="IonQuant Label-Free Quantification"> <param name="rt_tol" type="float" value="" min="0" optional="true" label="RT Window (minutes)"/> @@ -734,8 +944,96 @@ #set $prfx = $wf.quant_ms1.label_free_quantification #if $prfx.label_free_quantification_run == 'no' #set $wfdict['quantitation.run-label-free-quant'] = 'false' + #set $wfdict['ionquant.run-ionquant'] = 'false' + #set $wfdict['freequant.run-freequant'] = 'false' + #elif $prfx.label_free_quantification_run == 'ionquant' + #set $wfdict['quantitation.run-label-free-quant'] = 'true' + #set $wfdict['ionquant.run-ionquant'] = 'true' + #set $wfdict['freequant.run-freequant'] = 'false' + #set $cxt = $prfx.ionquant + #if $cxt.mbr_select != 'None' + #set $wfdict['ionquant.mbr'] = $cxt.mbr_select + #end if + #if $cxt.normalization != 'None' + #set $wfdict['ionquant.normalization'] = $cxt.normalization + #end if + #set $cxt = $prfx.ionquant.feature_detection + #if $cxt.mztol != '' + #set $wfdict['ionquant.mztol'] = $cxt.mztol + #end if + #if $cxt.rttol != '' + #set $wfdict['ionquant.rttol'] = $cxt.rttol + #end if + #if $cxt.imtol != '' + #set $wfdict['ionquant.imtol'] = $cxt.imtol + #end if + #set $cxt = $prfx.ionquant.mbr + #if $cxt.mbrrttol != '' + #set $wfdict['ionquant.mbrrttol'] = $cxt.mbrrttol + #end if + #if $cxt.mbrimtol != '' + #set $wfdict['ionquant.mbrimtol'] = $cxt.mbrimtol + #end if + #if $cxt.mbrmincorr != '' + #set $wfdict['ionquant.mbrmincorr'] = $cxt.mbrmincorr + #end if + #if $cxt.mbrtoprun != '' + #set $wfdict['ionquant.mbrtoprun'] = $cxt.mbrtoprun + #end if + #if $cxt.ionfdr != '' + #set $wfdict['ionquant.ionfdr'] = $cxt.ionfdr + #end if + #if $cxt.peptidefdr != '' + #set $wfdict['ionquant.peptidefdr'] = $cxt.peptidefdr + #end if + #if $cxt.proteinfdr != '' + #set $wfdict['ionquant.proteinfdr'] = $cxt.proteinfdr + #end if + #set $cxt = $prfx.ionquant.topn + #if $cxt.tp != '' + #set $wfdict['ionquant.tp'] = $cxt.tp + #end if + #if $cxt.minfreq != '' + #set $wfdict['ionquant.minfreq'] = $cxt.minfreq + #end if + #set $cxt = $prfx.ionquant.labeling_conditional + #if $cxt.labeling_option == 'labeling' + #set $cxt = $prfx.ionquant.labeling_conditional.labeling + #set $wfdict['ionquant.use-labeling'] = 'true' + #set $wfdict['ionquant.use-lfq'] = 'false' + #set $wfdict['ionquant.light'] = $cxt.light + #set $wfdict['ionquant.medium'] = $cxt.medium + #set $wfdict['ionquant.heavy'] = $cxt.heavy + #set $wfdict['ionquant.requantify'] = $cxt.requantify + #else + #set $cxt = $prfx.ionquant.labeling_conditional.lfq + #set $wfdict['ionquant.use-labeling'] = 'false' + #set $wfdict['ionquant.use-lfq'] = 'true' + #if $cxt.maxlfq != 'None' + #set $wfdict['ionquant.maxlfq'] = $cxt.maxlfq + #end if + #if $cxt.minions != '' + #set $wfdict['ionquant.minions'] = $cxt.minions + #end if + #end if + #set $cxt = $prfx.ionquant.advanced + #if $cxt.excludemods != '' + #set $wfdict['ionquant.excludemods'] = $cxt.excludemods + #end if + #if $cxt.minscans != '' + #set $wfdict['ionquant.minscans'] = $cxt.minscans + #end if + #if $cxt.minisotopes != '' + #set $wfdict['ionquant.minisotopes'] = $cxt.minisotopes + #end if + #if $cxt.locprob != '' + #set $wfdict['ionquant.locprob'] = $cxt.locprob + #end if + #if $cxt.writeindex != 'None' + #set $wfdict['ionquant.writeindex'] = $cxt.writeindex + #end if #elif $prfx.label_free_quantification_run == 'freequant' - #set $wfdict['quantitation.run-label-free-quant'] = 'false' + #set $wfdict['quantitation.run-label-free-quant'] = 'true' #set $wfdict['ionquant.run-ionquant'] = 'false' #set $wfdict['freequant.run-freequant'] = 'true' #set $cxt = $prfx.freequant @@ -796,9 +1094,11 @@ <conditional name="glycan_conditional"> <param name="use_glycan_composition" type="select" label="Perform Isobaric Quantification"> <option value="default">Use workflow defaults</option> + <option value="no">no</option> <option value="yes">yes</option> </param> <when value="default"/> + <when value="no"/> <when value="yes"> <param name="mod_tag" type="select" optional="true" label="PTM Mod tag"> <option value="none">none</option> @@ -885,7 +1185,6 @@ #set $wfdict['tmtintegrator.run-tmtintegrator'] = 'false' #elif $prfx.isobaric_quantification_step == 'yes' #set $wfdict['tmtintegrator.run-tmtintegrator'] = 'true' - #set $wfdict['tmtintegrator.dont-run-fq-lq'] = 'false' #set $cxt = $prfx.options #set $wfdict['tmtintegrator.quant_level'] = $cxt.quant_level #set $wfdict['tmtintegrator.channel_num'] = $cxt.channel_num @@ -895,14 +1194,17 @@ #set $wfdict['tmtintegrator.add_Ref'] = 1 #set $wfdict['tmtintegrator.ref_tag'] = $cxt.ref_tag #end if - #if $cxt.groupby != '' + #if $cxt.groupby != 'None' #set $wfdict['tmtintegrator.groupby'] = $cxt.groupby #end if #set $wfdict['tmtintegrator.log2transformed'] = $cxt.log2transformed #if $cxt.prot_norm != 'None' #set $wfdict['tmtintegrator.prot_norm'] = $cxt.prot_norm #end if - #if $cxt.glycan_conditional.use_glycan_composition == 'yes' + #if $cxt.glycan_conditional.use_glycan_composition == 'no' + #set $wfdict['tmtintegrator.use_glycan_composition'] = 'false' + #elif $cxt.glycan_conditional.use_glycan_composition == 'yes' + #set $wfdict['tmtintegrator.use_glycan_composition'] = 'true' #if $cxt.glycan_conditional.mod_tag != 'None' #set $wfdict['tmtintegrator.mod_tag'] = $cxt.glycan_conditional.mod_tag #end if @@ -970,18 +1272,110 @@ #end if ]]></token> + <xml name="dia_pseuedo_ms2" token_expand="false" token_yes="false" token_no="true"> + <section name="dia_pseudo" expanded="@EXPAND@" title="DIA Pseudo MS2"> + <conditional name="diatracer"> + <param name="diatracer_step" type="select" label="Run diaTracer"> + <option value="default">Use workflow defaults</option> + <option value="yes" selected="@YES@">yes</option> + <option value="no" selected="@NO@">no</option> + </param> + <when value="default"/> + <when value="no"/> + <when value="yes"> + <section name="options" expanded="true" title="diaPASEF Spectrum Deconvolution"> + <param name="corr_threshold" type="float" value="0.3" label="Corr Threshold"/> + <param name="delta_apex_im" type="float" value="0.01" label="Delta Apex IM"/> + <param name="delta_apex_rt" type="integer" value="3" label="Delta Apex RT"/> + <param name="rf_max" type="integer" value="500" label="RF max" /> + <param name="mass_defect_offset" type="float" value="0.1" label="Mass Defect Offset"/> + <param name="mass_defect_filter" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Mass Defect Filter"/> + </section> + </when> + </conditional> + </section> + </xml> + <token name="@DIA_PSEUDO_MS2@"><![CDATA[ +#set $prfx = $wf.dia_pseudo.diatracer +#if $prfx.diatracer_step == 'no' + #set $wfdict['diatracer.run-diatracer'] = 'false' +#elif $prfx.diatracer_step == 'yes' + #set $wfdict['diatracer.run-diatracer'] = 'true' + #set $cxt = $prfx.options + #set $wfdict['diatracer.corr-threshold'] = $cxt.corr_threshold + #set $wfdict['diatracer.delta-apex-im'] = $cxt.delta_apex_im + #set $wfdict['diatracer.delta-apex-rt'] = $cxt.delta_apex_rt + #set $wfdict['diatracer.rf-max'] = $cxt.rf_max + #set $wfdict['diatracer.mass-defect-offset'] = $cxt.mass_defect_offset + #set $wfdict['diatracer.mass-defect-filter'] = $cxt.mass_defect_filter +#end if +]]></token> + + <xml name="diann_quantification" token_expand="false" token_yes="true" token_no="false"> + <section name="quant_dia" expanded="@EXPAND@" title="Quant (DIA)"> + <conditional name="diann_quantification"> + <param name="diann_quantification_step" type="select" label="Perform DIA Quantification with DIA-NN"> + <option value="default">Use workflow defaults</option> + <option value="yes" selected="@YES@">yes</option> + <option value="no" selected="@NO@">no</option> + </param> + <when value="default"/> + <when value="no"/> + <when value="yes"> + <section name="options" expanded="true" title="Isobaric Quantification"> + <param name="qvalue" type="float" value="0.01" min="0.0" max="1.0" optional="true" label="Precursor FDR" help="default 0.01"/> + <param name="generate_msstats" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Generate MSStats input"/> + <param name="unrelated_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Unrelated runs"/> + <param name="use_predicted_spectra" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Replace library spectra with predicted"/> + <param name="library" type="data" format="csv,tsv,xls,txt,binary" optional="true" label="Spectral Library"/> + <param name="quantification_strategy" type="select" optional="true" label="Quantification strategy" help="default: Robust LC (high precision)"> + <option value="0">Any LC (high accuracy)</option> + <option value="1">Any LC (high precision)</option> + <option value="2">Robust LC (high accuracy)</option> + <option value="3">Robust LC (high precision)</option> + </param> + </section> + </when> + </conditional> + </section> + </xml> + <token name="@DIANN_QUANTIFICATION@"><![CDATA[ +#set $prfx = $wf.quant_dia.diann_quantification +#if $prfx.diann_quantification_step == 'no' + #set $wfdict['diann.run-dia-nn'] = 'false' +#elif $prfx.diann_quantification_step == 'yes' + #set $wfdict['diann.run-dia-nn'] = 'true' + #set $cxt = $prfx.options + #if $cxt.qvalue != '' + #set $wfdict['diann.q-value'] = $cxt.qvalue + #end if + #set $wfdict['diann.generate-msstats'] = $cxt.generate_msstats + #set $wfdict['diann.unrelated-runs'] = $cxt.unrelated_runs + #set $wfdict['diann.use-predicted-spectra'] = $cxt.use_predicted_spectra + #if $cxt.quantification_strategy != '' + #set $wfdict['diann.quantification-strategy'] = $cxt.quantification_strategy + #end if + #if $cxt.library + ln -s '$cxt.library' './diann_lib.speclib' + #set $wfdict['diann.library'] = 'diann_lib.speclib' + #end if +#end if +]]></token> + + + <!-- License agreement texts. --> <token name="@MSFRAGGER_LICENSE_AGREEMENT@"> -MSFragger is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: http://msfragger-upgrader.nesvilab.org/upgrader/MSFragger-LICENSE.pdf. This license provides with non-exclusive, non-transferable right to use MSFragger solely for academic research, non-commercial or educational purposes. I agree to be subject to the terms and conditions of this license. I understand that to use MSFragger for other purposes requires a commercial license from the University of Michigan Office of Tech Transfer. +MSFragger is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: http://msfragger-upgrader.nesvilab.org/upgrader/LICENSE-ACADEMIC.pdf. This license provides with non-exclusive, non-transferable right to use MSFragger solely for academic research, non-commercial or educational purposes. I agree to be subject to the terms and conditions of this license. I understand that to use MSFragger for other purposes requires a commercial license from the University of Michigan Office of Tech Transfer. </token> <token name="@IONQUANT_LICENSE_AGREEMENT@"> -IonQuant is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf +IonQuant is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: https://msfragger-upgrader.nesvilab.org/ionquant/LICENSE-ACADEMIC.pdf </token> <token name="@THERMO_RAW_READER_LICENSE_AGREEMENT@"> I agree to the terms of Thermo (c) Raw File Reader License Agreement: http://msfragger-upgrader.nesvilab.org/upgrader/RawFileRdr_License_Agreement_RevA.pdf </token> <token name="@BRUKER_LICENSE_AGREEMENT@"> -I agree to the terms of Bruker SDK library distribution conditions: http://msfragger-upgrader.nesvilab.org/upgrader/redist.txt +I agree to the terms of Bruker SDK library distribution conditions: http://msfragger-upgrader.nesvilab.org/upgrader/EULA%20TDF-SDK.pdf </token> <token name="@LICENSE_AGREEMENTS@"> @MSFRAGGER_LICENSE_AGREEMENT@