--- a/sr_bowtie_dataset_annotation.xml	Sun Oct 24 23:52:11 2021 +0000
+++ b/sr_bowtie_dataset_annotation.xml	Sat Apr 09 22:45:21 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.5.0">
+<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.6">
   <description>by iterative alignments with sRbowtie</description>
   <requirements>
         <requirement type="package" version="1.3.1">bowtie</requirement>
@@ -59,9 +59,11 @@
             remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
             echo -e "$sample\tNot classified\t\${remaining}\t\${genome_aligned}" >> $output &&
         #end for
-        
-        
         Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot
+        #if $format == '-q':
+            && mv class_unmatched.fa class_unmatched.fastq
+            && sed -n '1~4s/^@/>/p;2~4p' class_unmatched.fastq > class_unmatched.fa
+        #end if
         ]]></command>
   <inputs>
     <param name="input" type="data" multiple="True" format="fasta,fastq" label="Input file: reads clipped from their adapter" help="Only with clipped, raw fasta or fastq files"/>
@@ -94,6 +96,7 @@
 <!-- End of other bowtie index selections -->
    </inputs>
    <outputs>
+       <data format="fasta" name="unmatched" label="Annotate smRNAs: Unmatched reads" from_work_dir="class_unmatched.fa" />
        <data format="tabular" name="output" label="Cascade Annotation Analysis">
            <actions>
                <action name="column_names" type="metadata" default="Sample,Reference Index,Number of reads, Total reads" />
@@ -110,6 +113,7 @@
             <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
             <output name="output" ftype="tabular" file="sample1_output.tab" />
             <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/>
+            <output name="unmatched" ftype="fasta" file="unmatched_1.fa" />
         </test>
         <test>
             <param name="input" value ="sample.fastq" ftype="fastq" />
@@ -119,6 +123,7 @@
             <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
             <output name="output" ftype="tabular" file="sample_output.tab" />
             <output name="barplot" ftype="pdf" file="sample_output.pdf" compare="sim_size" delta="500"/>
+            <output name="unmatched" ftype="fasta" file="unmatched_2.fa" />
         </test>
         <test>
             <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" />
@@ -128,6 +133,7 @@
             <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
             <output name="output" ftype="tabular" file="multisample5_output.tab" />
             <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" />
+            <output name="unmatched" ftype="fasta" file="unmatched_3.fa" />
         </test>
     </tests>
   <help>
@@ -172,7 +178,16 @@
 
 **OUTPUTS**
 
-**Annotation table in a tabular format**
+**- Annotation table in a tabular format**
+
+**- Pie Charts of class abundances**
+
+**- Unmatched reads in fasta format**
 
   </help>
+
+  <citations>
+    <citation type="doi">10.1038/nature11416</citation>
+  </citations>
+
 </tool>