--- a/proteomiqon_proteininference.xml	Mon Jul 26 13:34:26 2021 +0000
+++ b/proteomiqon_proteininference.xml	Fri Apr 29 19:29:14 2022 +0000
@@ -13,6 +13,8 @@
         #if $PSMInputModeCond.PSMInputMode == "single"
             #set basename = $re.sub(r'[^\w ,.\-+]','_',$PSMInputModeCond.scoredPSMs.element_identifier)
             ln -s '$scoredPSMs' '${basename}.qpsm' &&
+            mkdir './out' &&
+            ln -s '$out_prot' './out/${basename}.prot' &&
         #elif $PSMInputModeCond.PSMInputMode == "multi"
             #for $psmfile in $PSMInputModeCond.scoredPSMs
                 #set basename = $re.sub(r'[^\w ,.\-+]','_',$psmfile.element_identifier)
@@ -36,7 +38,11 @@
                 "Peptide": {
                   "Case": "${Peptide}"
                 },
-                "GroupFiles": ${GroupFiles},
+                #if $PSMInputModeCond.PSMInputMode == "multi"
+                "GroupFiles": ${PSMInputModeCond.GroupFiles},
+                #else
+                "GroupFiles": false,
+                #end if
                 #if $GetQValueCond.GetQValue == "LogisticRegression"
                 "GetQValue": {
                   "Case": "${GetQValueCond.GetQValue}",
@@ -67,6 +73,7 @@
             </when>
             <when value="multi">
                 <param name="scoredPSMs" type="data" format="tabular" label="Scored PSM files" help="Specify list of peptide identifications." multiple="true"/>
+                <param name="GroupFiles" type="boolean" checked="true" label="Groupe files" help="If checked, protein inference is carried out using peptide information from all files simultaneously."/>
             </when>
         </conditional>
         <param name="ProteinIdentifierRegex" type="text" value="id" label="Protein identifier regex pattern" help="Fasta headers do often contain additional information in addition to your protein identifier, by specifying a regex pattern the tool can extract the protein IDs. If you fasta headers are already cleaned you can leave this field empty.">
@@ -81,7 +88,6 @@
             <option value="Maximal">Maximal</option>
             <option value="MaximalInverse">MaximalInverse</option>
         </param>
-        <param name="GroupFiles" type="boolean" checked="true" label="Groupe files" help="If checked, protein inference is carried out using peptide information from all files simultaneously."/>
         <conditional name="GetQValueCond">
             <param name="GetQValue" type="select" label="Q-Value method" help="Specify if and how q-value calculation should be carried out.">
                 <option value="Storey" selected="true">Storey</option>
@@ -102,8 +108,12 @@
     </inputs>
     <outputs>
         <data format="tabular" name="out_prot" >
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.prot" ext="tabular" directory="out" visible="true"  assign_primary_output="true" />
+            <filter>PSMInputModeCond['PSMInputMode'] == 'single'</filter>
         </data>
+        <collection type="list" format="tabular" name="out_prot_collection" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\.prot)" directory="out" />
+            <filter>PSMInputModeCond['PSMInputMode'] == 'multi'</filter>
+        </collection>
         <data format="json" name="out_paramfile">
             <filter>outputParamfile</filter>
         </data>
@@ -118,7 +128,6 @@
             <param name="ProteinIdentifierRegex" value="id"/>
             <param name="Protein" value="Minimal"/>
             <param name="Peptide" value="Minimal"/>
-            <param name="GroupFiles" value="true"/>
             <param name="outputParamfile" value="false"/>
         </test>
         <test expect_num_outputs="2">
@@ -130,7 +139,6 @@
             <param name="ProteinIdentifierRegex" value="id"/>
             <param name="Protein" value="Maximal"/>
             <param name="Peptide" value="Maximal"/>
-            <param name="GroupFiles" value="true"/>
             <conditional name="GetQValueCond">
                 <param name="GetQValue" value="Storey"/>
             </conditional>
@@ -146,7 +154,6 @@
             <param name="ProteinIdentifierRegex" value="id"/>
             <param name="Protein" value="Minimal"/>
             <param name="Peptide" value="MaximalInverse"/>
-            <param name="GroupFiles" value="true"/>
             <conditional name="GetQValueCond">
                 <param name="GetQValue" value="NoQValue"/>
             </conditional>
@@ -162,7 +169,6 @@
             <param name="ProteinIdentifierRegex" value="id"/>
             <param name="Protein" value="Minimal"/>
             <param name="Peptide" value="MaximalInverse"/>
-            <param name="GroupFiles" value="true"/>
             <conditional name="GetQValueCond">
                 <param name="GetQValue" value="LogisticRegression"/>
                 <param name="LogisticRegressionType" value="Conservative"/>
@@ -179,7 +185,6 @@
             <param name="ProteinIdentifierRegex" value="id"/>
             <param name="Protein" value="Minimal"/>
             <param name="Peptide" value="MaximalInverse"/>
-            <param name="GroupFiles" value="true"/>
             <conditional name="GetQValueCond">
                 <param name="GetQValue" value="LogisticRegression"/>
                 <param name="LogisticRegressionType" value="MAYU"/>
@@ -196,7 +201,6 @@
             <param name="ProteinIdentifierRegex" value="id"/>
             <param name="Protein" value="Minimal"/>
             <param name="Peptide" value="MaximalInverse"/>
-            <param name="GroupFiles" value="true"/>
             <conditional name="GetQValueCond">
                 <param name="GetQValue" value="LogisticRegression"/>
                 <param name="LogisticRegressionType" value="DecoyTargetRatio"/>
@@ -218,13 +222,14 @@
                 <param name="GetQValue" value="NoQValue"/>
             </conditional>
             <param name="outputParamfile" value="true"/>
+            <output_collection name="out_prot_collection" type="list" count="3" />
             <output name="out_paramfile" file="result_6.json" />
         </test>
         <test expect_num_outputs="2">
             <param name="peptideDB" value="sample.db"/>
             <conditional name="PSMInputModeCond">
                 <param name="PSMInputMode" value="multi"/>
-                <param name="scoredPSMs" value="sample_1.qpsm,sample_2.qpsm,sample_3.qpsm"/>
+                <param name="scoredPSMs" value="sample_1.qpsm,sample_2.qpsm"/>
             </conditional>
             <param name="ProteinIdentifierRegex" value="id"/>
             <param name="Protein" value="Maximal"/>
@@ -234,6 +239,7 @@
                 <param name="GetQValue" value="NoQValue"/>
             </conditional>
             <param name="outputParamfile" value="true"/>
+            <output_collection name="out_prot_collection" type="list" count="2" />
             <output name="out_paramfile" file="result_7.json" />
         </test>
     </tests>
@@ -266,4 +272,4 @@
 Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html>`_.  
     ]]>
     </help>
-</tool>
\ No newline at end of file
+</tool>