# HG changeset patch
# User galaxyp
# Date 1738433528 0
# Node ID 048390db193255ebe5231ac3602da509ced050bb
# Parent  e969a182e3cb10695cfcb152e62324907dc50a6a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 1dd092b0008017e57b66775f1763f824d100ca08

diff -r e969a182e3cb -r 048390db1932 macros.xml
--- 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'
diff -r e969a182e3cb -r 048390db1932 msfragger_macros.xml
--- 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