--- a/rna_quast.xml	Wed Jan 10 13:24:53 2024 +0000
+++ b/rna_quast.xml	Fri Aug 30 13:23:03 2024 +0000
@@ -13,16 +13,16 @@
     mkdir -p './fasta_files/' &&
     #import os, re, glob
     #for $i in $transcripts        
-        ln -s '$i' '${re.sub('[^\w\-.]', '_', i.element_identifier)}' &&
+        ln -s '$i' '${re.sub('[^\w.]', '_', i.element_identifier)}' &&
     #end for
     #if $reference
         #for $rf in $reference
-            ln -s '$rf' '${re.sub('[^\w\-.]', '_', rf.element_identifier)}' &&
+            ln -s '$rf' '${re.sub('[^\w.]', '_', rf.element_identifier)}' &&
         #end for
     #end if
     #if $gene_coordinates.selector == "true"
         #for $g in $gene_coordinates.gtf
-            ln -s '$g' '${re.sub('[^\w\-.]', '_', g.element_identifier)}' &&
+            ln -s '$g' '${re.sub('[^\w.]', '_', g.element_identifier)}' &&
         #end for
     #end if    
     mkdir outputdir &&
@@ -30,7 +30,7 @@
     --threads \${GALAXY_SLOTS:-8}
     --transcripts
     #for $i in $transcripts
-         '${re.sub('[^\w\-.]', '_', i.element_identifier)}'
+         '${re.sub('[^\w.]', '_', i.element_identifier)}'
     #end for
     #if $reads_option.selector == 'paired'
         --left_reads '${reads_option.forward_reads}'
@@ -45,13 +45,13 @@
     #if $reference
         -r
         #for $rf in $reference
-            '${re.sub('[^\w\-.]', '_', rf.element_identifier)}'
+            '${re.sub('[^\w.]', '_', rf.element_identifier)}'
         #end for
     #end if
     #if $gene_coordinates.selector == "true"
         --gtf
         #for $g in $gene_coordinates.gtf
-            '${re.sub('[^\w\-.]', '_', g.element_identifier)}'
+            '${re.sub('[^\w.]', '_', g.element_identifier)}'
         #end for
         $gene_coordinates.disable_infer_genes
         $gene_coordinates.disable_infer_transcripts
@@ -82,7 +82,7 @@
     #end if
     
     #if len($transcripts) == 1
-        #set $path = "/".join(['outputdir',($transcripts[0].element_identifier).split(".")[0]]) + "_output"
+        #set $path = "/".join(['outputdir',re.sub('[^\w.]', '_', $transcripts[0].element_identifier).split(".")[0]]) + "_output"
         && mv '${path}' './results'
         ## rename .list files to .txt files to make them detectable
         && find './results/' -name "*.list" -exec mv {} {}.txt \;
@@ -99,7 +99,7 @@
         && mkdir -p './results/'
         #if $gene_coordinates.selector == 'true' and $reference
             #for $i, $transcript in enumerate($transcripts)
-                #set $path = "/".join(['outputdir',($transcripts[$i].element_identifier).split(".")[0]]) + "_output"
+                #set $path = "/".join(['outputdir',re.sub('[^\w.]', '_', $transcripts[$i].element_identifier).split(".")[0]]) + "_output"
                 && rm -r ./results
                 && cp -r $path './results'
                 && mv ./results/*fasta './fasta_files/'
@@ -385,7 +385,7 @@
         </test>
         <!-- Test 08: Multiple inputs-->
         <test expect_num_outputs="6">
-            <param name="transcripts" value="transcriptome01.fasta,transcriptome02.fasta"/>
+            <param name="transcripts" value="transcriptome01.fasta,transcriptome?02.fasta"/>
             <param name="reference" value="reference.fasta"/>
             <conditional name="gene_coordinates">
                 <param name="selector" value="true"/>
@@ -407,7 +407,7 @@
                 <param name="single_reads" value="single_end.fastq.gz"/>
             </conditional>
             <output name="short_report_tabular" value="test_08_short_report.tab" ftype="tabular"/>
-            <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf"/>
+            <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
             <output name="stats" value="test_08_complete_report.tab" ftype="txt"  lines_diff="6" />
             <output_collection name="fasta_files" type="list" count="14">
                 <element name="transcriptome01.paralogs" file="test_08_paralogs.fasta" ftype="fasta"/>
@@ -432,7 +432,55 @@
                 </element>
             </output_collection>
         </test>
-
+        <!-- Test 09: Multiple inputs with dash in names-->
+        <test expect_num_outputs="6">
+            <param name="transcripts" value="transcriptome01.fasta,transcriptome-02.fasta"/>
+            <param name="reference" value="reference.fasta"/>
+            <conditional name="gene_coordinates">
+                <param name="selector" value="true"/>
+                <param name="gtf" value="reference.gtf"/>
+            </conditional>
+            <section name="output_options">
+                <param name="out_sr" value="tabular,pdf"/>
+            </section>
+            <conditional name="use_busco">
+                <param name="selector" value="true"/>
+                <conditional name="lineage_conditional">
+                    <param name="selector" value="cached"/>
+                    <param name="cached_db" value="busco-demo-db-20230328"/>
+                </conditional>
+            </conditional>
+            <param name="out_add" value="complete,fasta,logs,gz"/>
+            <conditional name="reads_option">
+                <param name="selector" value="single"/>
+                <param name="single_reads" value="single_end.fastq.gz"/>
+            </conditional>
+            <output name="short_report_tabular" value="test_08_short_report.tab" ftype="tabular"/>
+            <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
+            <output name="stats" value="test_08_complete_report.tab" ftype="txt"  lines_diff="6" />
+            <output_collection name="fasta_files" type="list" count="14">
+                <element name="transcriptome01.paralogs" file="test_08_paralogs.fasta" ftype="fasta"/>
+            </output_collection>
+            <output_collection name="list_logs" type="list" count="14">
+                <element name="STAR.out" ftype="txt">
+                    <assert_contents>
+                        <has_text text="STAR --runThreadN"/>
+                        <has_text text="finished successfully"/>
+                    </assert_contents>
+                </element>
+                <element name="gmap_build.out" ftype="txt">
+                    <assert_contents>
+                        <has_text text="No alternate scaffolds observed"/>
+                    </assert_contents>
+                </element>
+                <element name="rnaQUAST" ftype="txt">
+                    <assert_contents>
+                        <has_text text="THE QUALITY OF TRANSCRIPTOME ASSEMBLY DONE"/>
+                        <has_text text="Thank you for using rnaQUAST!"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[