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comparison macros.xml @ 5:048390db1932 draft default tip

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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
comparison
equal deleted inserted replaced
4:e969a182e3cb 5:048390db1932
1 <macros> 1 <macros>
2 <import>msfragger_macros.xml</import> 2 <import>msfragger_macros.xml</import>
3 <token name="@TOOL_VERSION@">20.0</token> 3 <token name="@TOOL_VERSION@">20.0</token>
4 <token name="@VERSION_SUFFIX@">4</token> 4 <token name="@VERSION_SUFFIX@">5</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
8 </requirements> 8 </requirements>
9 </xml> 9 </xml>
714 <section name="quant_ms1" expanded="@EXPAND@" title="Quant (MS1)"> 714 <section name="quant_ms1" expanded="@EXPAND@" title="Quant (MS1)">
715 <conditional name="label_free_quantification"> 715 <conditional name="label_free_quantification">
716 <param name="label_free_quantification_run" type="select" label="Perform Label-Free Quantification"> 716 <param name="label_free_quantification_run" type="select" label="Perform Label-Free Quantification">
717 <option value="default" selected="true">Use workflow default</option> 717 <option value="default" selected="true">Use workflow default</option>
718 <option value="no">No Label-Free Quantification</option> 718 <option value="no">No Label-Free Quantification</option>
719 <option value="ionquant">Run IonQuant</option>
720 <option value="freequant">Run FreeQuant</option> 719 <option value="freequant">Run FreeQuant</option>
721 </param> 720 </param>
722 <when value="default"/> 721 <when value="default"/>
723 <when value="no"/> 722 <when value="no"/>
724 <when value="ionquant">
725 <section name="ionquant" expanded="false" title="IonQuant Label-Free Quantification">
726 <param name="mbr_select" type="select" optional="true" label="Match between runs (MBR)" help="ionquant.mbr">
727 <option value="0">No</option>
728 <option value="1">Yes</option>
729 </param>
730 <param name="normalization" type="select" optional="true" label="Normalize" help="ionquant.normalization">
731 <option value="0">No</option>
732 <option value="1">Yes</option>
733 </param>
734 <section name="feature_detection" expanded="false" title="Feature detection">
735 <param name="mztol" type="integer" value="" optional="true" label="m/z tolerance in ppm" help="ionquant.mztol (default 10)"/>
736 <param name="rttol" type="float" value="" optional="true" label="RT tolerance (minutes)" help="ionquant.rttol (default 0.4)"/>
737 <param name="imtol" type="float" value="" optional="true" label="IM tolerance (1/k0)" help="ionquant.imtol (default 0.05)"/>
738 </section>
739 <section name="mbr" expanded="false" title="Match between runs (MBR)">
740 <param name="mbrrttol" type="float" value="" optional="true" label="MBR RT tolerance (minutes)" help="ionquant.mbrrttol"/>
741 <param name="mbrimtol" type="float" value="" optional="true" label="MBR IM tolerance (1/k0)" help="ionquant.mbrimtol"/>
742 <param name="mbrmincorr" type="float" value="" optional="true" label="MBR min correlation" help="ionquant.mbrmincorr"/>
743 <param name="mbrtoprun" type="integer" value="" optional="true" label="MBR top runs" help="ionquant.mbrtoprun"/>
744 <param name="ionfdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR ion FDR" help="ionquant.ionfdr"/>
745 <param name="peptidefdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR peptide FDR" help="ionquant.peptidefdr"/>
746 <param name="proteinfdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR protein FDR" help="ionquant.proteinfdr"/>
747 </section>
748 <section name="topn" expanded="false" title="Top-N options">
749 <param name="tp" type="integer" value="" min="0" optional="true" label="Top N ions" help="ionquant.tp"/>
750 <param name="minfreq" type="float" value="" min="0.0" max="1.0" optional="true" label="Min freq" help="ionquant.minfreq"/>
751 <param name="minexps" type="integer" value="" optional="true" label="Min exps" help="ionquant.minexps"/>
752 </section>
753 <conditional name="labeling_conditional">
754 <param name="labeling_option" type="select" label="Labeling option">
755 <option value="lfq" selected="true">LFQ</option>
756 <option value="labeling">Labeling</option>
757 </param>
758 <when value="lfq">
759 <section name="lfq" expanded="false" title="LFQ">
760 <param name="maxlfq" type="select" optional="true" label="MaxLFQ" help="ionquant.maxlfq">
761 <option value="0">No</option>
762 <option value="1">Yes</option>
763 </param>
764 <param name="minions" type="integer" value="" optional="true" label="Min ions" help="ionquant.minions"/>
765 </section>
766 </when>
767 <when value="labeling">
768 <section name="labeling" expanded="false" title="Labeling-based quant">
769 <param name="light" type="select" label="Light" help="ionquant.light">
770 <option value="" selected="true">none</option>
771 <option value="C463.2366">C463.2366</option>
772 <option value="C464.28596">C464.28596</option>
773 <option value="C561.3387">C561.3387</option>
774 <option value="K0;R0">K0;R0</option>
775 </param>
776 <param name="medium" type="select" label="Medium" help="ionquant.medium">
777 <option value="" selected="true">none</option>
778 <option value="K4.025107;R6.020129">K4.025107;R6.020129</option>
779 </param>
780 <param name="heavy" type="select" label="Heavy" help="ionquant.heavy">
781 <option value="" selected="true">none</option>
782 <option value="C467.2529">C467.2529</option>
783 <option value="C470.29977">C470.29977</option>
784 <option value="C567.3462">C567.3462</option>
785 <option value="K8.014199;R10.008269">K8.014199;R10.008269</option>
786 </param>
787 <param name="requantify" type="select" label="Re-quantify" help="ionquant.requantify">
788 <option value="0">No</option>
789 <option value="1" selected="true">Yes</option>
790 </param>
791 </section>
792 </when>
793 </conditional>
794 <section name="advanced" expanded="false" title="Advanced options">
795 <param name="excludemods" type="text" optional="true" label="excludemods" help="ionquant.excludemods">
796 <validator type="regex">^\s*@RE_EXCLUDEMODS@\s*$</validator>
797 </param>
798 <param name="minscans" type="integer" value="" min="0" optional="true" label="Min scans" help="ionquant.minscans"/>
799 <param name="minisotopes" type="integer" value="" min="1" max="3" optional="true" label="Min isotopes" help="ionquant.minisotopes"/>
800 <param name="locprob" type="float" value="" min="0.0" max="1.0" optional="true" label="Min site probability" help="ionquant.locprob"/>
801 <param name="writeindex" type="select" optional="true" label="Write index" help="ionquant.writeindex">
802 <option value="0">No</option>
803 <option value="1">Yes</option>
804 </param>
805 </section>
806 </section>
807 </when>
808 <when value="freequant"> 723 <when value="freequant">
809 <section name="freequant" expanded="false" title="IonQuant Label-Free Quantification"> 724 <section name="freequant" expanded="false" title="IonQuant Label-Free Quantification">
810 <param name="rt_tol" type="float" value="" min="0" optional="true" label="RT Window (minutes)"/> 725 <param name="rt_tol" type="float" value="" min="0" optional="true" label="RT Window (minutes)"/>
811 <param name="mz_tol" type="integer" value="" min="1" optional="true" label="m/z Window (ppm)"/> 726 <param name="mz_tol" type="integer" value="" min="1" optional="true" label="m/z Window (ppm)"/>
812 </section> 727 </section>
818 <!-- Set label-free quantification workflow options --> 733 <!-- Set label-free quantification workflow options -->
819 <token name="@LABEL_FREE_QUANTIFICATION@"><![CDATA[ 734 <token name="@LABEL_FREE_QUANTIFICATION@"><![CDATA[
820 #set $prfx = $wf.quant_ms1.label_free_quantification 735 #set $prfx = $wf.quant_ms1.label_free_quantification
821 #if $prfx.label_free_quantification_run == 'no' 736 #if $prfx.label_free_quantification_run == 'no'
822 #set $wfdict['quantitation.run-label-free-quant'] = 'false' 737 #set $wfdict['quantitation.run-label-free-quant'] = 'false'
823 #elif $prfx.label_free_quantification_run == 'ionquant'
824 #set $wfdict['quantitation.run-label-free-quant'] = 'false'
825 #set $wfdict['ionquant.run-ionquant'] = 'true'
826 #set $wfdict['freequant.run-freequant'] = 'false'
827 #set $cxt = $prfx.ionquant
828 #if $cxt.mbr_select != 'None'
829 #set $wfdict['ionquant.mbr'] = $cxt.mbr_select
830 #end if
831 #if $cxt.normalization != 'None'
832 #set $wfdict['ionquant.normalization'] = $cxt.normalization
833 #end if
834 #set $cxt = $prfx.ionquant.feature_detection
835 #if $cxt.mztol != ''
836 #set $wfdict['ionquant.mztol'] = $cxt.mztol
837 #end if
838 #if $cxt.rttol != ''
839 #set $wfdict['ionquant.rttol'] = $cxt.rttol
840 #end if
841 #if $cxt.imtol != ''
842 #set $wfdict['ionquant.imtol'] = $cxt.imtol
843 #end if
844 #set $cxt = $prfx.ionquant.mbr
845 #if $cxt.mbrrttol != ''
846 #set $wfdict['ionquant.mbrrttol'] = $cxt.mbrrttol
847 #end if
848 #if $cxt.mbrimtol != ''
849 #set $wfdict['ionquant.mbrimtol'] = $cxt.mbrimtol
850 #end if
851 #if $cxt.mbrmincorr != ''
852 #set $wfdict['ionquant.mbrmincorr'] = $cxt.mbrmincorr
853 #end if
854 #if $cxt.mbrtoprun != ''
855 #set $wfdict['ionquant.mbrtoprun'] = $cxt.mbrtoprun
856 #end if
857 #if $cxt.ionfdr != ''
858 #set $wfdict['ionquant.ionfdr'] = $cxt.ionfdr
859 #end if
860 #if $cxt.peptidefdr != ''
861 #set $wfdict['ionquant.peptidefdr'] = $cxt.peptidefdr
862 #end if
863 #if $cxt.proteinfdr != ''
864 #set $wfdict['ionquant.proteinfdr'] = $cxt.proteinfdr
865 #end if
866 #set $cxt = $prfx.ionquant.topn
867 #if $cxt.tp != ''
868 #set $wfdict['ionquant.tp'] = $cxt.tp
869 #end if
870 #if $cxt.minfreq != ''
871 #set $wfdict['ionquant.minfreq'] = $cxt.minfreq
872 #end if
873 #if $cxt.minexps != ''
874 #set $wfdict['ionquant.minexps'] = $cxt.minexps
875 #end if
876 #set $cxt = $prfx.ionquant.labeling_conditional
877 #if $cxt.labeling_option == 'labeling'
878 #set $cxt = $prfx.ionquant.labeling_conditional.labeling
879 #set $wfdict['ionquant.use-labeling'] = 'true'
880 #set $wfdict['ionquant.use-lfq'] = 'false'
881 #set $wfdict['ionquant.light'] = $cxt.labeling.light
882 #set $wfdict['ionquant.medium'] = $cxt.labeling.medium
883 #set $wfdict['ionquant.heavy'] = $cxt.labeling.heavy
884 #set $wfdict['ionquant.requantify'] = $cxt.labeling.requantify
885 #else
886 #set $cxt = $prfx.ionquant.labeling_conditional.lfq
887 #set $wfdict['ionquant.use-labeling'] = 'false'
888 #set $wfdict['ionquant.use-lfq'] = 'true'
889 #if $cxt.maxlfq != 'None'
890 #set $wfdict['ionquant.maxlfq'] = $cxt.maxlfq
891 #end if
892 #if $cxt.minions != ''
893 #set $wfdict['ionquant.minions'] = $cxt.minions
894 #end if
895 #end if
896 #set $cxt = $prfx.ionquant.advanced
897 #if $cxt.excludemods != ''
898 #set $wfdict['ionquant.excludemods'] = $cxt.excludemods
899 #end if
900 #if $cxt.minscans != ''
901 #set $wfdict['ionquant.minscans'] = $cxt.minscans
902 #end if
903 #if $cxt.minisotopes != ''
904 #set $wfdict['ionquant.minisotopes'] = $cxt.minisotopes
905 #end if
906 #if $cxt.locprob != ''
907 #set $wfdict['ionquant.locprob'] = $cxt.locprob
908 #end if
909 #if $cxt.writeindex != 'None'
910 #set $wfdict['ionquant.writeindex'] = $cxt.writeindex
911 #end if
912 #elif $prfx.label_free_quantification_run == 'freequant' 738 #elif $prfx.label_free_quantification_run == 'freequant'
913 #set $wfdict['quantitation.run-label-free-quant'] = 'false' 739 #set $wfdict['quantitation.run-label-free-quant'] = 'false'
914 #set $wfdict['ionquant.run-ionquant'] = 'false' 740 #set $wfdict['ionquant.run-ionquant'] = 'false'
915 #set $wfdict['freequant.run-freequant'] = 'true' 741 #set $wfdict['freequant.run-freequant'] = 'true'
916 #set $cxt = $prfx.freequant 742 #set $cxt = $prfx.freequant