# HG changeset patch
# User dfornika
# Date 1574797705 0
# Node ID e479272681a61d5e408f24c919b414aa7ee1bf83
# Parent  8fc05ce77eb710bee5258b4fd1eca9f5de2da03c
Uploaded

diff -r 8fc05ce77eb7 -r e479272681a6 tetyper.xml
--- a/tetyper.xml	Tue Nov 26 00:07:23 2019 +0000
+++ b/tetyper.xml	Tue Nov 26 19:48:25 2019 +0000
@@ -47,6 +47,15 @@
         <data name="log" format="text" from_work_dir="output.log" label="${tool.name} on ${on_string}: log"/>
     </outputs>
     <tests>
+        <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" />
+                <output name="summary" file="output_summary.txt" />
+            </conditional>
+        </test>
     </tests>
     <help>
       <![CDATA[
@@ -58,33 +67,33 @@
 
 TETyper will produce a tab-seperated output file with the following outputs:
 
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
-|  Column                  | Description                                                                                                                              |
-+==========================+==========================================================================================================================================+
-|  Deletions               | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. |
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
-|  Structural_variant      |                                                                                                                                          |
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
-|  SNPs_homozygous         |                                                                                                                                          |
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
-|  SNPs_heterozygous       |                                                                                                                                          |
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
-|  Heterozygous_SNP_counts |                                                                                                                                          |
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
-|  SNP_variant             |                                                                                                                                          |
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
-|  Combined_variant        |                                                                                                                                          |
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
-|  Left_flanks             |                                                                                                                                          |
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
-|  Right_flanks            |                                                                                                                                          |
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
-|  Left_flank_counts       |                                                                                                                                          |
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
-|  Right_flank_counts      |                                                                                                                                          |
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
-|  X_Y_presence            |                                                                                                                                          |
-+--------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|  Column                  | Description                                                                                                                                                                                                                                      |
++==========================+==================================================================================================================================================================================================================================================+
+|  Deletions               | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions.                                                                                                         |
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|  Structural_variant      | If --struct_profiles is specified and the pattern of deletions above corresponds to one of these profiles, then the profile name is given, otherwise "unknown".                                                                                  |
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|  SNPs_homozygous         | A list of homozygous SNPs identified, or "none".                                                                                                                                                                                                 |
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|  SNPs_heterozygous       | A list of heterozygous SNPs identified, or "none".                                                                                                                                                                                               |
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|  Heterozygous_SNP_counts | For each heterozygous SNP, the number of reads supporting the reference and alternative calls, or "none" if there are no heterozygous SNPs.                                                                                                      |
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|  SNP_variant             | If --snp_profiles is specified and the pattern of homozygous and heterozygous SNPs corresponds to one of these profiles, then the profile name is given. Otherwise "unknown".                                                                    |
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|  Combined_variant        | Single name combining Structural_variant and SNP_variant, separated by "-".                                                                                                                                                                      |
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|  Left_flanks             | A list of distinct sequences passing quality filters that flank the start position of the reference.                                                                                                                                             |
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|  Right_flanks            | A list of distinct sequences passing quality filters that flank the end position of the reference.                                                                                                                                               |
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|  Left_flank_counts       | The number of high quality reads supporting each of the left flanking sequences.                                                                                                                                                                 |
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|  Right_flank_counts      | The number of high quality reads supporting each of the right flanking sequences.                                                                                                                                                                |
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+|  X_Y_presence            | If --show_region is specified as --show_region X-Y, this column shows 1 if the entirety of that region is classified as present (i.e. no overlap with deleted regions), or 0 otherwise. If --show_region is unspecified, this column is omitted. |
++--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 
       ]]>
     </help>