# HG changeset patch
# User mheinzl
# Date 1616161824 0
# Node ID eca1365eb42c26a435d8157cf2d3dd70e2daff0b
# Parent  c44475567466eb30f377c095a25ebd1f8ed114e6
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

diff -r c44475567466 -r eca1365eb42c read2mut.py
--- a/read2mut.py	Thu Mar 18 11:09:51 2021 +0000
+++ b/read2mut.py	Fri Mar 19 13:50:24 2021 +0000
@@ -1134,7 +1134,6 @@
                         #                        'format': format2,
                         #                        'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)})
                         change_tier_after_print.append((row, line, line2, trimmed_actual_high_tier))
-
                         row += 3
 
             if chimera_correction:
diff -r c44475567466 -r eca1365eb42c test-data/SSCS_counts_test.json
--- a/test-data/SSCS_counts_test.json	Thu Mar 18 11:09:51 2021 +0000
+++ b/test-data/SSCS_counts_test.json	Fri Mar 19 13:50:24 2021 +0000
@@ -1,1 +1,1 @@
-[{"ACH_TDII_5regions#570": {"ab": 1, "ba": 1}, "ACH_TDII_5regions#504": {"ab": 2, "ba": 1}, "ACH_TDII_5regions#957": {"ab": 1, "ba": 1}}, {"ACH_TDII_5regions#570": {"ab": 2, "ba": 1}, "ACH_TDII_5regions#504": {"ab": 1, "ba": 1}, "ACH_TDII_5regions#957": {"ab": 1}}]
\ No newline at end of file
+[{"ACH_TDII_5regions#957#T#C": {"ab": 1, "ba": 1}, "ACH_TDII_5regions#504#C#A": {"ab": 2, "ba": 1}, "ACH_TDII_5regions#570#C#T": {"ab": 1, "ba": 1}}, {"ACH_TDII_5regions#957#T#C": {"ab": 1}, "ACH_TDII_5regions#504#C#A": {"ab": 1, "ba": 1}, "ACH_TDII_5regions#570#C#T": {"ab": 2, "ba": 1}}]
\ No newline at end of file
diff -r c44475567466 -r eca1365eb42c test-data/Variant_Analyzer_allele_frequencies_test.xlsx
Binary file test-data/Variant_Analyzer_allele_frequencies_test.xlsx has changed
diff -r c44475567466 -r eca1365eb42c test-data/Variant_Analyzer_summary_test.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Variant_Analyzer_summary_test.csv	Fri Mar 19 13:50:24 2021 +0000
@@ -0,0 +1,7 @@
+variant ID,tier,tag,mate,read pos.ab,read pos.ba,read median length.ab,read median length.ba,DCS median length,FS.ab,FS.ba,FSqc.ab,FSqc.ba,ref.ab,ref.ba,alt.ab,alt.ba,rel. ref.ab,rel. ref.ba,rel. alt.ab,rel. alt.ba,na.ab,na.ba,lowq.ab,lowq.ba,trim.ab,trim.ba,SSCS alt.ab,SSCS alt.ba,SSCS ref.ab,SSCS ref.ba,in phase,chimeric tag
+ACH_TDII_5regions-505-C-A,2.1,GATAACCTTGCTTCGTGATTAATC,ab1.ba2,132.0,131.0,264.0,263.0,173.0,1,3,1,3,0,0,1,3,0,0,1.0,1.0,0,0,0,0,0,0,2,1,1,1,,
+,,GATAACCTTGCTTCGTGATTAATC,ab2.ba1,,,,,173.0,0,0,0,0,0,0,0,0,,,,,0,0,0,0,0,0,2,1,1,1,,
+ACH_TDII_5regions-571-C-T,1.1,GATTGGATAACGTTGTGGCAATTG,ab1.ba2,129.0,218.0,195.0,284.0,143.0,4,5,4,5,0,0,4,5,0,0,1.0,1.0,0,0,0,0,0,0,1,1,2,1,,
+,,GATTGGATAACGTTGTGGCAATTG,ab2.ba1,264.0,264.0,278.5,283.5,143.0,2,2,2,2,0,0,2,2,0,0,1.0,1.0,0,0,0,0,0,0,1,1,2,1,,
+ACH_TDII_5regions-958-T-C,2.4,CCTCCCGGCAGTGCGAAAATGTCA,ab1.ba2,,,,,195.0,0,0,0,0,0,0,0,0,,,,,0,0,0,0,0,0,1,1,1,0,,
+,,CCTCCCGGCAGTGCGAAAATGTCA,ab2.ba1,97.0,91.0,283.0,277.0,195.0,1,1,1,1,0,0,1,1,0,0,1.0,1.0,0,0,0,0,0,0,1,1,1,0,,
diff -r c44475567466 -r eca1365eb42c test-data/Variant_Analyzer_summary_test.xlsx
Binary file test-data/Variant_Analyzer_summary_test.xlsx has changed
diff -r c44475567466 -r eca1365eb42c test-data/Variant_Analyzer_test.xlsx
Binary file test-data/Variant_Analyzer_test.xlsx has changed
diff -r c44475567466 -r eca1365eb42c test-data/Variant_Analyzer_tiers_test.xlsx
Binary file test-data/Variant_Analyzer_tiers_test.xlsx has changed
diff -r c44475567466 -r eca1365eb42c test-data/tag_count_dict_test.json
--- a/test-data/tag_count_dict_test.json	Thu Mar 18 11:09:51 2021 +0000
+++ b/test-data/tag_count_dict_test.json	Fri Mar 19 13:50:24 2021 +0000
@@ -1,1 +1,1 @@
-[{"GATAACCTTGCTTCGTGATTAATC": {"ACH_TDII_5regions#504": "A"}, "GATTGGATAACGTTGTGGCAATTG": {"ACH_TDII_5regions#570": "T"}, "CCTCCCGGCAGTGCGAAAATGTCA": {"ACH_TDII_5regions#957": "C"}}, {"ACH_TDII_5regions#570": [1, 1, 143.0], "ACH_TDII_5regions#504": [1, 1, 173.0], "ACH_TDII_5regions#957": [0, 1, 195.0]}]
\ No newline at end of file
+[{"GATAACCTTGCTTCGTGATTAATC": {"ACH_TDII_5regions#504#C#A": "A"}, "GATTGGATAACGTTGTGGCAATTG": {"ACH_TDII_5regions#570#C#T": "T"}, "CCTCCCGGCAGTGCGAAAATGTCA": {"ACH_TDII_5regions#957#T#C": "C"}}, {"ACH_TDII_5regions#957#T#C": [0, 1, 195.0], "ACH_TDII_5regions#504#C#A": [1, 1, 173.0], "ACH_TDII_5regions#570#C#T": [1, 1, 143.0]}]
\ No newline at end of file
diff -r c44475567466 -r eca1365eb42c va_macros.xml
--- a/va_macros.xml	Thu Mar 18 11:09:51 2021 +0000
+++ b/va_macros.xml	Fri Mar 19 13:50:24 2021 +0000
@@ -4,8 +4,15 @@
         <citation type="bibtex">
             @misc{duplex,
             author = {Povysil, Gundula and Heinzl, Monika and Salazar, Renato and Stoler, Nicholas and Nekrutenko, Anton and Tiemann-Boege, Irene},
-            year = {2019},
-            title = {{Variant Analyzer: a quality control for variant calling in duplex sequencing data (manuscript)}}
+            doi = {10.1093/nargab/lqab002},
+            issn = {2631-9268},
+            number = {1},
+            journal = {NAR Genomics and Bioinformatics},
+            publisher = {NAR Genomics and Bioinformatics},
+            title = {{Increased yields of duplex sequencing data by a series of quality control tools}}
+            url = {https://pubmed.ncbi.nlm.nih.gov/33575654},
+            volume = {3},
+            year = {2021}
          }
         </citation>
     </citations>