# HG changeset patch
# User dfornika
# Date 1574878353 0
# Node ID 2c41d192f4cc54bf2bf000de3870371b1ea67346
# Parent  3efdbbddd8598b96b9bdb492499ec7f503be4545
Uploaded

diff -r 3efdbbddd859 -r 2c41d192f4cc tetyper.xml
--- a/tetyper.xml	Tue Nov 26 23:46:30 2019 +0000
+++ b/tetyper.xml	Wed Nov 27 18:12:33 2019 +0000
@@ -75,7 +75,7 @@
                 <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" />
+            <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" />
             <output name="summary" file="output_summary_2.txt" />
         </test>
     </tests>
@@ -85,6 +85,44 @@
 
 TETyper is designed for typing a specific transposable element (TE) of interest from paired-end sequencing data. It determines single nucleotide variants (SNVs) and deletions within the TE, as well as flanking sequences surrounding the TE.
 
+**Input**
+
+**SNP Profiles**: A tab-delimited file with the following columns:
+
+1. Profile ID
+2. Homozygous SNPs
+3. Heterozygous SNPs
+
+SNPs are represented in the format [REF][POSITION][ALT], and separated by pipe (`|`) characters. SNPs should be ordered by position. Valid alt-bases for heterozygous SNPs are: `M,R,W,S,Y,K`
+
+For example:
+
+::
+
+  1	none	none
+  2	C8015T	none
+  3	C8015T|T9621C	none
+  4	T7199A|C8015T|T9621C	none
+  6	C7509G|T7917G	none
+  N2	none	C8015Y
+  N4	none	A5178R
+  N5	none	C8015Y|T9663Y
+
+**Structural Variant Profiles**: A tab-delimited file with the following columns:
+
+1. Profile ID
+2. Structural Variants
+
+Structural Variants are represented in the format [START-POSITION]-[END-POSITION], and separated by pipe (`|`) characters.
+
+For example:
+
+::
+  Tn4401b	none
+  Tn4401a	7020-7118
+  Tn4401h	6919-7106
+  Tn4401_truncC	1-7127|9198-10006
+
 **Output**
 
 TETyper will produce a tab-seperated output file with the following outputs: