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Merge pull request #787 from reid-wagner/digestion_and_ionquant_fixes
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FragPipe: Fix Digestion Options and Remove IonQuant
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@bgruening
bgruening authored Feb 1, 2025
2 parents f98d62a + 65ffdb2 commit 1dd092b
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Showing 2 changed files with 2 additions and 175 deletions.
176 changes: 1 addition & 175 deletions tools/fragpipe/macros.xml
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Original file line number Diff line number Diff line change
@@ -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>
Expand Down Expand Up @@ -716,95 +716,10 @@ $kv
<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)"/>
Expand All @@ -820,95 +735,6 @@ $kv
#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'
Expand Down
1 change: 1 addition & 0 deletions tools/fragpipe/msfragger_macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -986,6 +986,7 @@ Example (M oxidation and N-terminal acetylation):
#import re
#set $msfragger_dict = {}
@SEARCH_TOLERANCES@
@DIGESTION@
## Variable Modification Parameters sets $vmods
@VARIABLE_MODIFICATION@
## Static Modification Parameters sets $fmods
Expand Down

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