--- a/shigatyper.xml	Thu Jun 27 14:39:17 2019 -0400
+++ b/shigatyper.xml	Wed Jul 31 11:57:03 2019 -0400
@@ -4,20 +4,61 @@
         <requirement type="package" version="1.0.5">shigatyper</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        shigatyper -n "$input1.name" "$input1" "$input2" -vv > "$output1"
+        #if $reads.reads_select == 'collection'
+            #set forward=$reads.coll.forward
+            #set reverse=$reads.coll.reverse
+            #set name=$reads.coll.name
+        #else
+            #set name=$reads.coll.forward.name.split('_')[0]
+        #end if
+
+        shigatyper -n "$name" "$forward" "$reverse" -vv >
+
+        #if $reads.reads_select == 'collection'
+            ${serotype_from_collection}
+        #else
+            ${serotype_from_history}
+        #end if
     ]]></command>
     <inputs>
-        <param type="data" name="input1" format="fastqsanger, fastqsanger.gz" />
-        <param type="data" name="input2" format="fastqsanger, fastqsanger.gz" />
+        <conditional name="reads">
+            <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
+                <option value="collection">Paired collection from your history</option>
+                <option value="history">Two FASTQ datasets from your history</option>
+            </param>
+            <when value="collection">
+                <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
+            </when>
+            <when value="history">
+                <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
+                <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
+            </when>
+        </conditional>
     </inputs>
     <outputs>
-        <data name="output1" label="Shigella serotype prediction" format="tabular" />
+        <data label="${reads.coll.name} Shigella serotype determination" name="serotype_from_collection" format="sam">
+            <filter>reads['reads_select'] == 'collection'</filter>
+        </data>
+        <data label="${reads.forward.name.split('_')[0]} Shigella serotype determination" name="serotype_from_history" format="sam">
+            <filter>reads['reads_select'] == 'history'</filter>
+        </data>
     </outputs>
     <tests>
         <test>
-            <param name="input1" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/>
-            <param name="input2" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/>
-            <output name="output1" file="output.tabular"/>
+            <param name="reads_select" value="history" />
+            <param name="forward" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/>
+            <param name="reverse" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/>
+            <output name="serotype_from_history" file="output.tabular"/>
+        </test>
+        <test>
+            <param name="reads_select" value="collection" />
+            <param name="coll">
+                <collection type="paired">
+                    <element name="forward" value="CFSAN029786_S10_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" />
+                    <element name="reverse" value="CFSAN029786_S10_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" />
+                </collection>
+            </param>
+            <output name="serotype_from_collection" value="output.tabular" />
         </test>
     </tests>
     <help><![CDATA[
@@ -32,12 +73,12 @@
     <citations>
         <citation type="bibtex">
 @misc{githubshigatyper,
-  author = {LastTODO, FirstTODO},
-  year = {TODO},
-  title = {shigatyper},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  url = {https://github.com/CFSAN-Biostatistics/shigatyper},
+  author = Wu Y1, Lau HK, Lee T, Lau DK, Payne J.
+  year = 2019,
+  title = In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification,
+  publisher = AEM,
+  journal = Appl Environ Microbiol. ,
+  url = https://www.ncbi.nlm.nih.gov/pubmed/30709819,
 }</citation>
     </citations>
 </tool>
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