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Fix IonQuant Options in FragPipe #774

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merged 1 commit into from
Sep 12, 2024
Merged

Fix IonQuant Options in FragPipe #774

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1 change: 1 addition & 0 deletions tools/fragpipe/fragpipe.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -154,6 +154,7 @@
<param name="database_name" value="default/test.fasta" ftype="fasta"/>
<param name="manifest" value="default/test.manifest" ftype="tabular"/>
<param name="workflow_name" value="Default"/>
<param name="label_free_quantification_run" value="ionquant"/>
<param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/>
<param name="license_agreements" value="true"/>
<output name="concat_psm_tsv" ftype="tabular">
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11 changes: 4 additions & 7 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@">2</token>
<token name="@VERSION_SUFFIX@">3</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
Expand Down Expand Up @@ -719,7 +719,7 @@ $kv
<when value="no"/>
<when value="ionquant">
<section name="ionquant" expanded="false" title="IonQuant Label-Free Quantification">
<param name="mbr" type="select" optional="true" label="Match between runs (MBR)" help="ionquant.mbr">
<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>
Expand Down Expand Up @@ -821,11 +821,8 @@ $kv
#set $wfdict['ionquant.run-ionquant'] = 'true'
#set $wfdict['freequant.run-freequant'] = 'false'
#set $cxt = $prfx.ionquant
#if $cxt.mbr != 'None'
#set $wfdict['ionquant.mbr'] = $cxt.mbr
#end if
#if $cxt.maxlfqbr is not None
#set $wfdict['ionquant.maxlfqbr'] = $cxt.maxlfqbr
#if $cxt.mbr_select != 'None'
#set $wfdict['ionquant.mbr'] = $cxt.mbr_select
#end if
#if $cxt.normalization != 'None'
#set $wfdict['ionquant.normalization'] = $cxt.normalization
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