Mercurial > repos > galaxyp > fragpipe
changeset 5:048390db1932 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 1dd092b0008017e57b66775f1763f824d100ca08
| author | galaxyp |
|---|---|
| date | Sat, 01 Feb 2025 18:12:08 +0000 |
| parents | e969a182e3cb |
| children | |
| files | macros.xml msfragger_macros.xml |
| diffstat | 2 files changed, 2 insertions(+), 175 deletions(-) [+] |
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--- a/macros.xml Fri Dec 13 15:17:28 2024 +0000 +++ b/macros.xml Sat Feb 01 18:12:08 2025 +0000 @@ -1,7 +1,7 @@ <macros> <import>msfragger_macros.xml</import> <token name="@TOOL_VERSION@">20.0</token> - <token name="@VERSION_SUFFIX@">4</token> + <token name="@VERSION_SUFFIX@">5</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement> @@ -716,95 +716,10 @@ <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"/> - <param name="minexps" type="integer" value="" optional="true" label="Min exps" help="ionquant.minexps"/> - </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)"/> @@ -820,95 +735,6 @@ #set $prfx = $wf.quant_ms1.label_free_quantification #if $prfx.label_free_quantification_run == 'no' #set $wfdict['quantitation.run-label-free-quant'] = 'false' - #elif $prfx.label_free_quantification_run == 'ionquant' - #set $wfdict['quantitation.run-label-free-quant'] = 'false' - #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 - #if $cxt.minexps != '' - #set $wfdict['ionquant.minexps'] = $cxt.minexps - #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.labeling.light - #set $wfdict['ionquant.medium'] = $cxt.labeling.medium - #set $wfdict['ionquant.heavy'] = $cxt.labeling.heavy - #set $wfdict['ionquant.requantify'] = $cxt.labeling.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['ionquant.run-ionquant'] = 'false'
--- a/msfragger_macros.xml Fri Dec 13 15:17:28 2024 +0000 +++ b/msfragger_macros.xml Sat Feb 01 18:12:08 2025 +0000 @@ -986,6 +986,7 @@ #import re #set $msfragger_dict = {} @SEARCH_TOLERANCES@ + @DIGESTION@ ## Variable Modification Parameters sets $vmods @VARIABLE_MODIFICATION@ ## Static Modification Parameters sets $fmods