--- a/isoformswitchanalyzer.xml	Tue May 30 08:39:23 2023 +0000
+++ b/isoformswitchanalyzer.xml	Fri Jun 02 10:27:16 2023 +0000
@@ -20,6 +20,9 @@
            description="An undefined error occurred, please check your input carefully and contact your administrator." />
     </stdio>
     <command><![CDATA[
+            #set $conditions = list()
+            #set $sampleIDs = list()
+            #set $replicates = list()
             #if $functionMode.selector == 'data_import'
                 #if $functionMode.transcriptome.is_of_type("fasta.gz"):
                     ln -s '${functionMode.transcriptome}' './transcriptome.fasta.gz' &&
@@ -51,21 +54,35 @@
                             #set $stringtie_annotation = './stringtie_annotation.gtf' 
                         #end if
                     #end if
+                #else if $functionMode.tool_source.selector == 'salmon'
+                    #set $filename = 'quant.sf'
                 #else
-                    #set $filename = 'quant.sf'
+                    #set $filename = 'abundance.tsv'
                 #end if
 
-                #for $index in range(len($functionMode.first_factor.trans_counts)):
-                    mkdir './input_files/${functionMode.first_factor.factorLevel}${index}/' &&
-                    ln -s $functionMode.first_factor.trans_counts[$index] './input_files/${functionMode.first_factor.factorLevel}${index}/${filename}' &&
+                #for $index in range(len($functionMode.tool_source.first_factor.trans_counts)):
+                    $conditions.append($functionMode.tool_source.first_factor.factorLevel)
+                    $sampleIDs.append(str($functionMode.tool_source.first_factor.factorLevel) + str($index))
+                    $replicates.append($index)
+                    mkdir './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/' &&
+                    ln -s $functionMode.tool_source.first_factor.trans_counts[$index] './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/${filename}' &&
                 #end for
 
-                #for $index in range(len($functionMode.second_factor.trans_counts)):
-                    mkdir './input_files/${functionMode.second_factor.factorLevel}${index}/' &&
-                    ln -s $functionMode.second_factor.trans_counts[$index] './input_files/${functionMode.second_factor.factorLevel}${index}/${filename}' &&
+                #for $index in range(len($functionMode.tool_source.second_factor.trans_counts)):
+                    $conditions.append($functionMode.tool_source.second_factor.factorLevel)
+                    $sampleIDs.append(str($functionMode.tool_source.second_factor.factorLevel) + str($index))
+                    $replicates.append($index)
+                    mkdir './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/' &&
+                    ln -s $functionMode.tool_source.second_factor.trans_counts[$index] './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/${filename}' &&
                 #end for
                 
                 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R'
+                    #for $i, $condition in enumerate($conditions)
+                        --condition $condition
+                        --sampleID $sampleIDs[$i]
+                        --replicate $replicates[$i]
+                    #end for
+                    $functionMode.pairedSamples
                     --modeSelector $functionMode.selector
                     --parentDir './input_files'
                     --annotation $annotation
@@ -207,31 +224,20 @@
                 <option value="second_step">Analysis part two: Plot all isoform switches and their annotation</option>
             </param>
             <when value="data_import">
-                <section name="first_factor" title="1: Factor level" expanded="true">
-                    <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor' or 'treated'"
-                        help="Only letters, numbers and underscores will be retained in this field">
-                        <sanitizer>
-                            <valid initial="string.letters,string.digits"><add value="_" /></valid>
-                        </sanitizer>
-                    </param>
-                    <param name="trans_counts" type="data" format="tabular" multiple="true" label="Transcript-level expression measurements"/> 
-                </section>
-                <section name="second_factor" title="2: Factor level" expanded="true">
-                    <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor' or 'treated'"
-                        help="Only letters, numbers and underscores will be retained in this field">
-                        <sanitizer>
-                            <valid initial="string.letters,string.digits"><add value="_" /></valid>
-                        </sanitizer>
-                    </param>
-                    <param name="trans_counts" type="data" format="tabular" multiple="true" label="Transcript-level expression measurements"/> 
-                </section>
                 <conditional name="tool_source">
                     <param name="selector" type="select" label="Quantification data source"  help="IsoformSwitchAnalyzeR has different functions for importing data from different sources.">
                         <option value="stringtie">StringTie</option>
-                        <option value="salmon">Salmon/Kallisto</option>
+                        <option value="salmon">Salmon</option>
+                        <option value="kallisto">Kallisto</option>
                     </param>
-                    <when value="salmon"/>
+                    <when value="salmon">
+                        <expand macro="macro_inputs"/>
+                    </when>
+                    <when value="kallisto">
+                        <expand macro="macro_inputs"/>
+                    </when>
                     <when value="stringtie">
+                        <expand macro="macro_inputs"/>
                         <param name="averageSize" type="integer" min="0" value="150" label="Average read length" help="Must be the number of base pairs sequenced. e.g. if the data 
                         quantified is 75 bp paired ends the the user should supply readLength=75" />
                         <param argument="fixStringTieAnnotationProblem" type="boolean" truevalue="--fixStringTieAnnotationProblem" falsevalue="" checked="true" 
@@ -256,13 +262,14 @@
                     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 argument="pairedSamples" type="boolean" truevalue="--pairedSamples" falsevalue="" checked="false" label="Paired samples between factors" help="Samples 
+                    from different factors belong to the same individual (e.g. samples from same patient from health and cancerous tissues or different parts from the same plant)" />
                 <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-->
@@ -595,23 +602,23 @@
         </data>
     </outputs>
     <tests>
-        <!-- Test 01: Data import mode-->
+         <!-- Test 01: Data import mode-->
         <test expect_num_outputs="1">
             <conditional name="functionMode">
                 <param name="selector" value="data_import"/>
                 <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>
                 <param name="transcriptome" value="transcriptome.fasta.gz"/>
                 <param name="countFiles" value="disabled"/>
-                <section name="first_factor">
-                    <param name="factorLevel" value="health"/>
-                    <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
-                </section>
-                <section name="second_factor">
-                    <param name="factorLevel" value="cancer"/>
-                    <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
-                </section>
                 <conditional name="tool_source">
                     <param name="selector" value="salmon"/>
+                    <section name="first_factor">
+                        <param name="factorLevel" value="health"/>
+                        <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
+                    </section>
+                    <section name="second_factor">
+                        <param name="factorLevel" value="cancer"/>
+                        <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
+                    </section>
                 </conditional>
             </conditional>
             <output name="switchList" file="test01.RData" ftype="rdata" compare="sim_size" delta="100"/>
@@ -623,16 +630,16 @@
                 <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>
                 <param name="transcriptome" value="transcriptome.fasta.gz"/>
                 <param name="countFiles" value="matrix"/>
-                <section name="first_factor">
-                    <param name="factorLevel" value="health"/>
-                    <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
-                </section>
-                <section name="second_factor">
-                    <param name="factorLevel" value="cancer"/>
-                    <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
-                </section>
                 <conditional name="tool_source">
                     <param name="selector" value="salmon"/>
+                    <section name="first_factor">
+                        <param name="factorLevel" value="health"/>
+                        <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
+                    </section>
+                    <section name="second_factor">
+                        <param name="factorLevel" value="cancer"/>
+                        <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
+                    </section>
                 </conditional>
             </conditional>
             <output name="switchList" ftype="rdata">
@@ -650,16 +657,16 @@
                 <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>
                 <param name="transcriptome" value="transcriptome.fasta.gz"/>
                 <param name="countFiles" value="collection"/>
-                <section name="first_factor">
-                    <param name="factorLevel" value="health"/>
-                    <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
-                </section>
-                <section name="second_factor">
-                    <param name="factorLevel" value="cancer"/>
-                    <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
-                </section>
                 <conditional name="tool_source">
                     <param name="selector" value="salmon"/>
+                    <section name="first_factor">
+                        <param name="factorLevel" value="health"/>
+                        <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
+                    </section>
+                    <section name="second_factor">
+                        <param name="factorLevel" value="cancer"/>
+                        <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
+                    </section>
                 </conditional>
             </conditional>
             <output name="switchList" ftype="rdata">
@@ -668,10 +675,11 @@
                 </assert_contents>
             </output>
             <output_collection name="collection_counts_factor1" type="list" count="2">
-                <element name="cancer0_dataset" file="test03_cancer_counts.tabular" ftype="tabular" lines_diff="6"/>
+                <element name="health0_dataset" file="test03_health_counts.tabular" ftype="tabular" lines_diff="6"/>
+
             </output_collection>
             <output_collection name="collection_counts_factor2" type="list" count="2">
-                <element name="health0_dataset" file="test03_health_counts.tabular" ftype="tabular" lines_diff="6"/>
+                <element name="cancer0_dataset" file="test03_cancer_counts.tabular" ftype="tabular" lines_diff="6"/>
             </output_collection>
         </test>
         <!-- Test 04: Extract isoform switches all outputs-->
@@ -867,7 +875,7 @@
             </output>
             <output name="isoformFeatures" ftype="tabular">
                 <assert_contents>
-                    <has_size value="95185" delta="100"/>
+                    <has_size value="94888" delta="100"/>
                     <has_text text="gene_overall_mean"/>
                 </assert_contents>
             </output>
@@ -1039,7 +1047,7 @@
             </output>
             <output name="isoformFeatures" ftype="tabular">
                 <assert_contents>
-                    <has_size value="99607" delta="50"/>
+                    <has_size value="99310" delta="50"/>
                     <has_text text="gene_overall_mean"/>
                 </assert_contents>
             </output>
@@ -1061,6 +1069,54 @@
                 </assert_contents>
             </output>        
         </test>
+        <!-- Test 09: Kallisto input-->
+        <test expect_num_outputs="1">
+            <conditional name="functionMode">
+                <param name="selector" value="data_import"/>
+                <param name="genomeAnnotation" value="annotation_kallisto.gtf.gz"/>
+                <param name="transcriptome" value="transcriptome_kallisto.fasta.gz"/>
+                <param name="countFiles" value="disabled"/>
+                <conditional name="tool_source">
+                    <param name="selector" value="kallisto"/>
+                    <section name="first_factor">
+                        <param name="factorLevel" value="health"/>
+                        <param name="trans_counts" value="kallisto_cond1_rep1.tsv,kallisto_cond1_rep2.tsv"/>
+                    </section>
+                    <section name="second_factor">
+                        <param name="factorLevel" value="cancer"/>
+                        <param name="trans_counts" value="kallisto_cond2_rep1.tsv,kallisto_cond2_rep2.tsv"/>
+                    </section>
+                </conditional>
+            </conditional>
+            <output name="switchList" file="test09.RData" ftype="rdata" compare="sim_size" delta="100"/>
+        </test>
+        <!-- Test 10: Test paired samples in the experimental design-->
+        <test expect_num_outputs="3">
+            <conditional name="functionMode">
+                <param name="selector" value="data_import"/>
+                <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>
+                <param name="transcriptome" value="transcriptome.fasta.gz"/>
+                <param name="pairedSamples" value="true"/>
+                <param name="countFiles" value="matrix"/>
+                <conditional name="tool_source">
+                    <param name="selector" value="salmon"/>
+                    <section name="first_factor">
+                        <param name="factorLevel" value="health"/>
+                        <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
+                    </section>
+                    <section name="second_factor">
+                        <param name="factorLevel" value="cancer"/>
+                        <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
+                    </section>
+                </conditional>
+            </conditional>
+            <output name="switchList" ftype="rdata">
+                <assert_contents>
+                    <has_size value="652170" delta="300"/>
+                </assert_contents>
+            </output>
+            <output name="sample_annotation" file="test10_samples_annotation.tabular" ftype="tabular"/>
+        </test>
     </tests>
     <help><![CDATA[