Mercurial > repos > galaxyp > fragpipe
comparison macros.xml @ 3:da9ebef968bd draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit b1b03bb7cd31c1ec806b286d6c9444428b358e15
| author | galaxyp |
|---|---|
| date | Thu, 12 Sep 2024 08:06:44 +0000 |
| parents | ef46866326ef |
| children | e969a182e3cb |
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| 2:ef46866326ef | 3:da9ebef968bd |
|---|---|
| 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@">2</token> | 4 <token name="@VERSION_SUFFIX@">3</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> |
| 717 </param> | 717 </param> |
| 718 <when value="default"/> | 718 <when value="default"/> |
| 719 <when value="no"/> | 719 <when value="no"/> |
| 720 <when value="ionquant"> | 720 <when value="ionquant"> |
| 721 <section name="ionquant" expanded="false" title="IonQuant Label-Free Quantification"> | 721 <section name="ionquant" expanded="false" title="IonQuant Label-Free Quantification"> |
| 722 <param name="mbr" type="select" optional="true" label="Match between runs (MBR)" help="ionquant.mbr"> | 722 <param name="mbr_select" type="select" optional="true" label="Match between runs (MBR)" help="ionquant.mbr"> |
| 723 <option value="0">No</option> | 723 <option value="0">No</option> |
| 724 <option value="1">Yes</option> | 724 <option value="1">Yes</option> |
| 725 </param> | 725 </param> |
| 726 <param name="normalization" type="select" optional="true" label="Normalize" help="ionquant.normalization"> | 726 <param name="normalization" type="select" optional="true" label="Normalize" help="ionquant.normalization"> |
| 727 <option value="0">No</option> | 727 <option value="0">No</option> |
| 819 #elif $prfx.label_free_quantification_run == 'ionquant' | 819 #elif $prfx.label_free_quantification_run == 'ionquant' |
| 820 #set $wfdict['quantitation.run-label-free-quant'] = 'false' | 820 #set $wfdict['quantitation.run-label-free-quant'] = 'false' |
| 821 #set $wfdict['ionquant.run-ionquant'] = 'true' | 821 #set $wfdict['ionquant.run-ionquant'] = 'true' |
| 822 #set $wfdict['freequant.run-freequant'] = 'false' | 822 #set $wfdict['freequant.run-freequant'] = 'false' |
| 823 #set $cxt = $prfx.ionquant | 823 #set $cxt = $prfx.ionquant |
| 824 #if $cxt.mbr != 'None' | 824 #if $cxt.mbr_select != 'None' |
| 825 #set $wfdict['ionquant.mbr'] = $cxt.mbr | 825 #set $wfdict['ionquant.mbr'] = $cxt.mbr_select |
| 826 #end if | |
| 827 #if $cxt.maxlfqbr is not None | |
| 828 #set $wfdict['ionquant.maxlfqbr'] = $cxt.maxlfqbr | |
| 829 #end if | 826 #end if |
| 830 #if $cxt.normalization != 'None' | 827 #if $cxt.normalization != 'None' |
| 831 #set $wfdict['ionquant.normalization'] = $cxt.normalization | 828 #set $wfdict['ionquant.normalization'] = $cxt.normalization |
| 832 #end if | 829 #end if |
| 833 #set $cxt = $prfx.ionquant.feature_detection | 830 #set $cxt = $prfx.ionquant.feature_detection |