--- a/multiqc.xml	Wed Aug 08 08:49:39 2018 -0400
+++ b/multiqc.xml	Sun Jan 20 05:20:30 2019 -0500
@@ -1,7 +1,7 @@
 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@">
     <description>aggregate results from bioinformatics analyses into a single report</description>
     <macros>
-        <token name="@WRAPPER_VERSION@">1.6</token>
+        <token name="@WRAPPER_VERSION@">1.7</token>
         <token name="@ESCAPE_IDENTIFIER@">
 <![CDATA[
 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
@@ -372,6 +372,9 @@
                 @LN_3_FILES@
             #end if
         #end for
+    #elif str($repeat.software_cond.software) == "slamdunk"
+        #set $pattern = "# slamdunk"
+        @LN_FILES@
     #elif str($repeat.software_cond.software) == "snpeff"
         #set $pattern = "SnpEff_version"
         @LN_FILES@
@@ -539,7 +542,7 @@
                     <option value="samtools">Samtools</option>
                     <!--<option value="sargasso">Sargasso</option>-->
                     <!--<option value="skewer">Skewer</option>-->
-                    <!--<option value="slamdunk">Slamdunk</option>-->
+                    <option value="slamdunk">Slamdunk</option>
                     <option value="snpeff">SnpEff</option>
                     <option value="sortmerna">SortMeRNA</option>
                     <option value="star">STAR</option>
@@ -732,12 +735,15 @@
                         </conditional>
                     </repeat>
                 </when>
-                <when value="sortmerna">
-                    <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/>
+                <when value="slamdunk">
+                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of Slamdunk Alleyoop" help="It should contain '# slamdunk'"/>
                 </when>
                 <when value="snpeff">
                     <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/>
                 </when>
+                <when value="sortmerna">
+                    <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/>
+                </when>
                 <when value="star">
                     <repeat name="output" title="STAR output" min="1">
                         <conditional name="type">
@@ -846,6 +852,12 @@
             </repeat>
             <repeat name="results">
                 <conditional name="software_cond">
+                    <param name="software" value="slamdunk" />
+                    <param name="input" value="slamdunk_summary.txt,slamdunk_reads1_overallrates.csv,slamdunk_reads2_overallrates.csv" />
+                </conditional>
+            </repeat>
+            <repeat name="results">
+                <conditional name="software_cond">
                     <param name="software" value="sortmerna" />
                     <param name="input" value="sortmerna.txt" />
                 </conditional>
@@ -867,6 +879,7 @@
                     <has_text text="An ultra-fast all-in-one FASTQ preprocessor" />
                     <has_text text="fastqc_seq_heatmap_key_t" />
                     <has_text text="flexbar_plot" />
+                    <has_text text="a tool to analyze SLAMSeq data" />
                     <has_text text="sortmerna-detailed-plot" />
                     <has_text text="trimmomatic_plot" />
                 </assert_contents>
@@ -878,6 +891,7 @@
                 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/>
+                <element name="slamdunk_readrates_plus" file="slamdunk_readrates_plus.tabular" compare="sim_size" delta="10"/>
                 <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/>
                 <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/>
             </output_collection>