# HG changeset patch
# User dfornika
# Date 1574809401 0
# Node ID 010a346ee927117645fb942648dc2f8948c3cfa4
# Parent  e479272681a61d5e408f24c919b414aa7ee1bf83
Uploaded

diff -r e479272681a6 -r 010a346ee927 tetyper.xml
--- a/tetyper.xml	Tue Nov 26 19:48:25 2019 +0000
+++ b/tetyper.xml	Tue Nov 26 23:03:21 2019 +0000
@@ -41,6 +41,8 @@
         <param name="min_each_strand" type="integer" min="1" value="1" max="100" label="Minimum Reads (each strand)" help="Minimum read number for each strand for including a specific flanking sequence."/>
         <param name="min_mapped_len" type="integer" min="8" value="30" max="100" label="Minimum Mapped Length" help="Minimum length of mapping for a read to be used in determining flanking sequences. Higher values are more robust to spurious mapping. Lower values will recover more reads."/>
         <param name="min_qual" type="integer" min="0" value="10" max="100" label="Minimum quality" help="Minimum quality value across extracted flanking sequence." />
+        <param name="snp_profiles" type="data" format="text" label="SNP Profiles" />
+        <param name="struct_profiles" type="data" format="text" label="Structural Variant Profiles" />
     </inputs>
     <outputs>
         <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/>
@@ -53,8 +55,19 @@
                 <param name="selector" value="paired" />
                 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
                 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
-                <output name="summary" file="output_summary.txt" />
             </conditional>
+            <output name="summary" file="output_summary_1.txt" />
+        </test>
+        <test>
+            <param name="reference" value="Tn4401b-1.fasta" />
+            <conditional name="collection_paired">
+                <param name="selector" value="paired" />
+                <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
+                <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
+            </conditional>
+            <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" />
+            <param name="snp_profiles" value="Tn4401b_struct_profiles.txt" />
+            <output name="summary" file="output_summary_2.txt" />
         </test>
     </tests>
     <help>