--- a/isoformswitchanalyzer.xml	Fri May 19 21:25:39 2023 +0000
+++ b/isoformswitchanalyzer.xml	Wed May 24 06:06:36 2023 +0000
@@ -42,6 +42,15 @@
                 #end if
                 #if $functionMode.tool_source.selector == 'stringtie'
                     #set $filename = 't_data.ctab'
+                    #if $functionMode.tool_source.novoisoforms.selector == 'novel'
+                        #if $functionMode.tool_source.novoisoforms.stringtieAnnotation.is_of_type("gtf.gz"):
+                            ln -s '${$functionMode.tool_source.novoisoforms.stringtieAnnotation}' './stringtie_annotation.gtf.gz' &&
+                            #set $stringtie_annotation = './stringtie_annotation.gtf.gz' 
+                        #else
+                            ln -s '${$functionMode.tool_source.novoisoforms.stringtieAnnotation}' './stringtie_annotation.gtf' &&
+                            #set $stringtie_annotation = './stringtie_annotation.gtf' 
+                        #end if
+                    #end if
                 #else
                     #set $filename = 'quant.sf'
                 #end if
@@ -61,8 +70,12 @@
                     --parentDir './input_files'
                     --annotation $annotation
                     --transcriptome $transcriptome
+                    $functionMode.removeNonConvensionalChr
                     --toolSource $functionMode.tool_source.selector
                     #if $functionMode.tool_source.selector == 'stringtie'
+                        #if $functionMode.tool_source.novoisoforms.selector == 'novel'
+                            --stringtieAnnotation $stringtie_annotation
+                        #end if
                         --readLength $functionMode.tool_source.averageSize
                         $functionMode.tool_source.fixStringTieAnnotationProblem
                     #end if
@@ -224,18 +237,32 @@
                         <param argument="fixStringTieAnnotationProblem" type="boolean" truevalue="--fixStringTieAnnotationProblem" falsevalue="" checked="true" 
                             label="Fix StringTie annotation problem" help="This option will automatically try and correct some of the annoation problems created when 
                                 doing transcript assembly (unassigned transcripts and merged genes)" />
+                        <conditional name="novoisoforms">
+                            <param name="selector" type="select" label="Analsys mode">
+                                <option value="novel">Include novel isoforms in analysis</option>
+                                <option value="reference">Reference-only analysis</option>
+                            </param>
+                            <when value="novel">
+                                <param name="stringtieAnnotation" type="data" format="gtf,gtf.gz" label="Annotation generated by StringTie merge" 
+                                    help="The merged GTF is used to recalculate expression estimates using the merged, novel transcripts." />
+                            </when>
+                            <when value="reference"/>
+                        </conditional>
                     </when>
                 </conditional>
-                <param name="genomeAnnotation" type="data" format="gtf,gtf.gz" label="Genome annotation (GTF)" 
+                <param name="genomeAnnotation" type="data" format="gtf,gtf.gz" label="Genome annotation" 
                     help="It is used to integrate the coding sequence (CDS) regions from in the GTF file as the ORF regions used by IsoformSwitchAnalyzeR." />
                 <param name="transcriptome" type="data" format="fasta,fasta.gz" label="Transcriptome" 
                     help="Please note this different from a fasta file with the sequences of the entire genome." />
+                <param argument="removeNonConvensionalChr" type="boolean" truevalue="--removeNonConvensionalChr" falsevalue="" checked="false" 
+                    label="Remove non-conventional chromosomes" help="These regions are typically used to annotate regions that cannot be associated to a specific region." />
                 <param name="countFiles" type="select" label="Generate count matrix files" help="If IsoformSwitchAnalyzeR is used for fixing Stringtie annotation
                     problem, it can generate count files for analyzing differential expression with DESeq2 (when selecting collection) or CEMiTool (when secting the expression matrix format).">
                     <option value="disabled">Disabled</option>
                     <option value="collection">Collection of count files</option>
                     <option value="matrix">Expression matrix</option>
                 </param>
+
             </when>
 
             <!--WRAPPER FIRST STEP SECTION-->