# HG changeset patch
# User greg
# Date 1626976932 0
# Node ID 2286f3a13e4d9e8a2976d56f76bc69b513860e0f
# Parent  49aceeefab0a73bea7915605443ddbda14f39df8
Uploaded

diff -r 49aceeefab0a -r 2286f3a13e4d test-data/all_vcf2.fasta
--- a/test-data/all_vcf2.fasta	Fri Jun 18 18:12:16 2021 +0000
+++ b/test-data/all_vcf2.fasta	Thu Jul 22 18:02:12 2021 +0000
@@ -1,12 +1,6 @@
 >01_1787_FL_Zoo_Jaguar_vcf
-ATCTTGTGCAGCAGCCGGCGTCGTGTGACTATGGTCTGCGACTCTACGTGAGACTCTTGGCTGGTTCTCGGATCAGTCCATTTATGGCCACCTTCATGGGGTTCAAAACTACGCGGCTAAGCTGTCATACCAGATTGAGCACGGTGCGCGAACGCCCGATGAGCCACCGTCTTCGAAGGGCAAAATAGTCCCCCATTGGCACGCGTCCAGCCCGCAGGTGGTACGTTTGTCGTCAATACCACCACTAACACCAAATTAGCCACCTTCGAGGAGGCGTGGTAGGAGCGCGGTTGGTCACCCCATACCGTAAACAACGCTTTCGCAAGCACACGGACCCGTGCGTCATACCAGGCTTAGGACATGGTCTACATACGGCACGCTGCCAGGCAACGGTTGGTAATTTAAGCATACCGAGGAGAACACTCTCCCTTGCGGGGAACGACCTGCAGAGCCACGTAGTGACAGACCAGGCTCCGACTATTGGCAAAGTGTATTCTGAAGTGGGCCCGCACATTGTAGTTGTTAGTATCGAATAGAGCCCAGCGGTGTACGTCCAGCAATAGCTGAACATCCGAGGCATAATGGTTACAGTAGAATCCAAGTCTAACGTGGCACYTACGGCCACAGACTGACTAGGGGCTTTGGCTGGGGAACGAAATGTGTGATGACTTGCGGTATGGAGAGGGATCCGACCCGGTTCAGTAACAAGGTGGTCGTTCGCAGCGCGCTGCTATTTCCTGGACATGACACCTCTCCTCCACTGCGCAGCCTCTAAGGTACGTCCCTTGCGGCGCCCATTTTGACCCCACTATATCGACAGCGTCTTCACTCTGCTGCTACGTCC
 >BCG_Pasteur_Unknown_FR_SRR8886989_vcf
-GTNCCTNATGTNGATTAATGCAGCACTNTGATGGTCGATAC-TATNNCCNATNTCTCCGGCTCGC-NTCAACCGCCTATATNNGCGCGGGGCTCTGCTTGCAGCNGCNGCGGATNCGCGGCNNNNNNNTNTCGNGAAGCTGGGACCTGATGGNACCCCCCNGCCN-NAANTCGTAGTCTTTNCNGCGCCCNNNTGGCNAGTTGACCTT--TCTGTGNNCAGTNTACCCATTTCTGACGCGGNNGCNGGCGCCNNGNCGATCGACGCT-GGCCNATCCCACCNANAGCGAGTCAACNGNCTCGNGNTACGNCCGGAGACCTGNAGGACGANGACCTTCANGAGNGCTANGGAGTCGGAGGTNNTACGTGTGCGTTTTATCNCAGGGAACGATTACNAGCGGNTNGGGTGCNTTC--GNNGGCGTNTCGNTCNACTCCACGAACTAC-TGTGAAT-NAGGNCAGTGAGTAGGGTCCTAGGGGCCAATNAGGGGGGTTCTGAGCCACNTTTATCTGACTCGAGNNCGGACGCANAGCNAATNNAGAAANAGGCTNCTTGTGGGGGCYCAAGTGCANAAAANGGAGC-ACCGTGNTNGAANCTCNGCGCNGCAGACTGGTCGCAGTTGGGGGTTAGGTGNAAATCNCGGGCACAANGTGTGGGGCATGACCGACCAT-GCGCNGCAAGAGGCATAGTTTGTCTNGGCCGTGTACGTG--GTCTACCACGGNTNAGCACCCATTNNNTGCAGNGNTCCCNNTTCCGCACTAGGAGCACCGATCG-TCNTCNCATACCATTTAGCCTCAACTCATCACAAT-NAGNTTCTNTTGTCACAATCNCCNANGT
 >02_0585_COA_TX_Fed_vcf
-ATCTTGTGCGGCAGCCGGCGTCATGTGACTGCAAACTGCGACTCTACGTGGGACTCTTGGTCGGCTCCAGGATCAGGCCGTTTGTGCCCACCCTCATGGTGTTTAAAACTACGCGGCTAAGCTGTCATACCAAATTGGGCACAGTCCGCTAACACATCATGACTCGCCGTCTTCGGAGGGTACAATAGTTCCCCATTGGCACACGTCCAGCTCGCAGGTGGCACGTTTGCTGTTAATATCACCATTAACAATAAATTGGCTACCTCCGAGGAGGCGTGGTAGGAGCGCGGTCGGCCACTCCATACCGTAAATGACGCTTTCGCAAGCAAACGGACTTATTCCTCATGCCAGACTTAGGACATGGTCTACATACGTCACGCTGCCAAGCAACGGTTGGTAATTTAAGCACACCGGGGAGAGAATTCTCCCTTGTGGGGAAAGACCTGCGGAGCCACGTGGTGACAGACCATTCTACGACTATTAGCAGAATATATTCTGAAGTGGGCCCGTACATTGTAGGTGTTAGCACAGGACAGAGCCCAGCGGTATACGCCCAGGAATAGCTGAACGTCCGGGGCATGATGGTCACAGTAGTCTTCAAGTCTAACGTGGTAGYCACGGCCAGGAGCTGACTAGGGGCTTCGAGTGGGGAACAAAATGTGTAATGACTTGCGGCACGAAGGGGGGCCCGACCCAGCCCAATAACAAAGTGATCACCCGTAGACCGCTGCTGTTTCCGGGACATGACACCTTTCCTCCAGTGCGCAGACTATAAGGTACGTCCCTTGCAGGGCTCCGCTTGACCCGGTTATGTCNACAGCGTCTTCACTCTGCCGCTACGTCC
 >BCG_Tokyo_Unknown_JP_DRR029468_vcf
-GTGCCTCATGTAGATTAATGCAGCACTCTGATGGTCGATACCTATCTCCCATGTCCCCCGCTCGCCATCAACCGCCTATATCAGCGCGGGGCTCTGCTTGCAGCGGCGGCGGATACGCGGCACGGTGTTTTCGAGAAGCTGGGACCTGATGGTACCCCCCAGCCT-TAATTCGTAGTCTTTGCCGCGCCCCTCTGTCGAGTTGACCTTGGTCTACGTACATTGTACCCATTTCTGACGCGGCTGCCGGCGCCGGGCCGATCGACGCTAGGCCAATCCCACCAAGAGCGATCCAACCGTCTAGTGTTACGACCGGAGACCCGAAGGAAGAAGACCTTCACGAGGGCTAGGGAGCCGGAGGTGCTACGCGTACGTTTTGTCTCAGGGAACGGTTACGGTCGGTTCGGGTGCGTTCGAGGAGGCGTCTCGTTCTACTCCACGAACTACGTGTGAATCTAGGACAGTGAGCAGGGTCCTAGGGGCCAATGAGGGGGGTTCTGAGCCGCGTTTATCTGACTCGAGAGCGGACGCAAAGCAGGTTCAGAAAGAGGCTCCTTGTGGGGGCTCAGGNGCACAAAGGGGAGCAACCGTGAGGGAACCTCGGCGCGGTAGACTGGTCGCAATTGGGGGTCAGGTGCAAACCGCGGGCAGAAGGTGAGGGATACGACCAACCATAGCGCAGCAAGAGGCATAGTTTGTCTGGGCCGTGTACGTG--GTCTACCACGGGCCAGTACCCANTTTATGCAGCGGCCCCTTGTCCGCATGAGGAGCATCGATCGCTCCTCCCATACCATTCAGCCCCGATTCATCGCAATNCAGATTCTTCTGCCACAATCTCCGATGT
 >02_5877_MEX_TX_Fed_vcf
-ACCTTGTGCGGCAGCCGGCATCATGTGACTACAAATTGCGACCCCACGTGGGACTCTTGACTGACTCCAGGATCAGTCCAATTGTACCCACTCTCATGGTGTTCAAAACTACGCGGCTAAGCTGTCATACCAAATTGGGCACGGTCCTCTAACATACCATGACTCGCCGTCTTCGGAGGGTACAATAGTTCCCCATTGGCACGCGTCCAGCTCGCAGGTGGCACGTTTGTTGTTACTACCACCATTAATACTAAATTGGCYACGTCCGAAGAGGCGTGGTAGGAGCGCGGTCGGCCACTCCATACCGTAAATGACTCTTTCGCAAGCAAACGGACTCATGCCTCACGCCAGACTTAGCACATGGTCTACATACGTCACGCTGCCAAGGAACGGTTGGTAATCTAAACACACCGG-AAGAGAATTCTCCCTTGCGGGGAAAGACCTACGGAGCCACGTGGTGACAGACCATTCTCCGACTATTAGCAGAATGTACCTCAGAGTGGGCCCGTACATTGTAGGTGTTAGCACAGAACAGAGCCCAGCGGTATACGCCCAGGAATAGCTGAACGTCCGAGGCATGATGGTCACAGTAATCTTCAAATCTAACGTGGTAGYCATGGCCAGGGGCTGACCAGGGGCTTCAGGTGGGGAACGAAATGTGTACTGACTTGCGACACGGAGGAGAGCCCGACCCGGCCCAGTAACAAAGTGACCACCCGTAGACCGCTGCTATTTCCGGGACATGACACCTCTCCTCTAGTGCGCATACTATAAGGTACGTCCTTTGCAGCGCTCAGCTTGACCCCATTATATCGACAGCGTCTTCACTCTGCCGCTACGTCC
 >root
-ATCTTTTGCGTCAGCCGGCGCCGTGTGACTATGGTCGGCGATTCTACGTGAGACCCCTGGCTGGCTCTCGGATCACTCCATTTGTGCCCACCTTCGTGGGGATCAAAACTACGCGGGTGACCTATCAGACCCGGTTGGCCGCGGTCCGCTAACACCCCATGACCCGCCGCTTTCGGAGGGTACAGCAGTCGCTCATTAGCACGCGTCCGACCCGCAGGTGGTACATCCGTTGTTAACACCATCGCTAACACCAAATTGGCCACCTCCGGGCAGGCCTCATCGGAGCGGGGTCGGCGGCCTCGCACCGCAGACGGCGCCCTCGCAAGCAACCGGACTCATGCGTCATACCAGGCTTAGGACATGGTCTACATACGTCACGCTGCCAAGCAATGGTTGGTAACTTAAGCACACCGGGGAGGGCATTCCCCCTGGCGCCGATAGACATGTGGAGCCACGTGGTGGCAGACCAGGTTCTGGCTGTCAACAAGGTGTATTCTGAAGTGCCTTCGTACATTGCAAGGCTTAGCACAGAACCGAGCTCAACGATGTACGCCCAGGAAGAGCTGAATGTCTAAGGCAGAATGGTCACAGTAGAATCCAAGTCTAGCGTGGTAGCCACGGCCGGGGGCTGACTAGGGGCTTCGGGTGGGGAGCGAAATGTGTGATGACTTACGGCGCGGAGAGAGGCCCGGCCCGGCTCAGTAACAAACTGGTTGTCCGCAGCGCTCTGCCATTTCCTGGGCATGATACCTCTCCTCCAGTGCGCAGACCATAAGGCGTGTTCCTTGCAGCGCTCAGCCTGAACCCATTATATCAACAGCGCCGTTACTCTGCTGCTACGCGC
diff -r 49aceeefab0a -r 2286f3a13e4d test-data/all_vcf3.fasta
--- a/test-data/all_vcf3.fasta	Fri Jun 18 18:12:16 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
->01_1787_FL_Zoo_Jaguar_vcf
-ATCTTGTGCACAGCCGGCGTCGTGTGACTATGTGCGATCTACGTGAGACTCTTGGCGGTTCGGATCAGTCCATTATGGCCACTTCATGGGGTCAAAACTACGCGGCTAAGCTCAACCAGATTGAGCACGGTGCGCGAACGCCCGATGAGCCACCGTCTCGAAGGGCAAAATAGTCCCCCATTGGCACGCGTCGCCCGCAGGGTACGTTTGTCGTCAATACCACCACTAACACCAAATTAGCACCTTCGAGGAGGCGTGGTAGGAGGTTGGTCACCCCATACCGTAAACAACGCTTTCGCAAGCACACGGACCCGTGCGTCATACAGGCTTAGGACATGGTCTACATACGGCCGTGCCAGGCAACGGTTGGTAATTTAACATACCGGAGAACACTCTCCCTTGCGGGGAACGACCTGCAGAGCCCGTAGTGACAGACCAGGCTCCGACTATTGGCAAAGTGTATTCTGAAGGCGACATTGAGTTTAGTTCGAATAGAGCCAGCGGTGTACGTCCAGCAATAGCTGAAATCCGAGGCAAATGGTTACAGTAGAATCCAATCTAACGTGGCATACGGCCACAGACTGACTAGGGGCTTTGGCTGGGGAACGAAATGTGTGATGACTTGCGGTATGGAGAGGGATCCGACCCGGTTCAGTAACAAGTGGTCGTTCGCAGCGCGCTGCTATTTCCTGGACATGACACCTCTCCTCCACTGCGCAGCCTCTAAGGTAGTCCCTTGCGGCGCCCATTTTGACCCCACTATATCACAGCGTCTTCACTCTGCGCTACGTCC
->BCG_Pasteur_Unknown_FR_SRR8886989_vcf
-GTNCCTNATGNGATTAATGCAGCACTNTGATGGATACTATNNCCNATNTCTCCGGCCGC-NAACCGCCTATATNGCGCGGGGTCTGCTTGCGCNGCNGCGGATNCGCGGCNNNNTNTCGNGAAGCTGGGACCTGATGGNACCCCCCNGCCN-NAANTCTAGTCTTTNCNGCGCCCNNNTGGCNAGTTGACCT-TCTGTGNNGTNTACCCATTTCTGACGCGGNNGCNGGCGCCNNGNCGATGACGCT-GGCCNATCCCACCNANAGTCAACNGNCTCGNGNTACGNCCGGAGACCTGNAGGACGANGACCTTCANGAGNGCTAGGAGTCGGAGGTNNTACGTGTGCGTTTTTCCAGGGAACGATTACNAGCGGNTNGGTGCNTTCGNNGGCGTNTCGNTCNACTCCACGAACTAC-TGTGAATNAGGNCAGTGAGTAGGGTCCTAGGGGCCAATNAGGGGGGTTCTGAGACTACTGACTGAGCGGACCANAGCNAATNAGAAANAGGCTNCTTGTGGGGGCYCAAGGCANAAAANGAGC-ACCGTGNTNGAANCTCNCGCNGCAGACTGCGCAGTTGGGGGTTAGGTGNAAATCNCGGGCACAANGTGTGGGGCATGACCGACCAT-GCGCNGCAAGAGGCATAGTTTGTCTNGGCCGTGTAGTG--GTCTACCACGGNTNAGCACCCATTNNNTGCAGNGNTCCCNNTTCCGCACTAGGAGCACCGATCGTCNTCNCATACCATTTAGCCTCAACTCATCACAATNAGNTTCTNTTGTCACAACNCCNANGT
->02_0585_COA_TX_Fed_vcf
-ATCTTGTGCGCAGCCGGCGTCATGTGACTGCATGCGATCTACGTGGGACTCTTGGTGGCTCGGATCAGGCCGTTGTGCCCACCTCATGGTGTTAAAACTACGCGGCTAAGCTCAACCAAATTGGGCACAGTCCGCTAACACATCATGACTCGCCGTCTCGGAGGGTACAATAGTTCCCCATTGGCACACGTCGCTCGCAGGGCACGTTTGCTGTTAATATCACCATTAACAATAAATTGGCACCTCCGAGGAGGCGTGGTAGGAGGTCGGCCACTCCATACCGTAAATGACGCTTTCGCAAGCAAACGGACTTATTCCTCATGCAGACTTAGGACATGGTCTACATACGTCCGTGCCAAGCAACGGTTGGTAATTTAACACACCGGAGAGAATTCTCCCTTGTGGGGAAAGACCTGCGGAGCCCGTGGTGACAGACCATTCTACGACTATTAGCAGAATATATTCTGAAGGCGACATTGAGGTTAGCCAGGACAGAGCCAGCGGTATACGCCCAGGAATAGCTGAAGTCCGGGGCAGATGGTCACAGTAGTCTTCAATCTAACGTGGTACACGGCCAGGAGCTGACTAGGGGCTTCGAGTGGGGAACAAAATGTGTAATGACTTGCGGCACGAAGGGGGGCCCGACCCAGCCCAATAACAAATGATCACCCGTAGACCGCTGCTGTTTCCGGGACATGACACCTTTCCTCCAGTGCGCAGACTATAAGGTAGTCCCTTGCAGGGCTCCGCTTGACCCGGTTATGTCACAGCGTCTTCACTCTGCGCTACGTCC
->BCG_Tokyo_Unknown_JP_DRR029468_vcf
-GTGCCTCATGAGATTAATGCAGCACTCTGATGGATACTATCTCCCATGTCCCCCGCCGCCAAACCGCCTATATCGCGCGGGGTCTGCTTGCGCGGCGGCGGATACGCGGCACTGTTTCGAGAAGCTGGGACCTGATGGTACCCCCCAGCCT-TAATTCTAGTCTTTGCCGCGCCCCTCTGTCGAGTTGACCTGTCTACGTATTGTACCCATTTCTGACGCGGCTGCCGGCGCCGGGCCGATGACGCTAGGCCAATCCCACCAAGATCCAACCGTCTAGTGTTACGACCGGAGACCCGAAGGAAGAAGACCTTCACGAGGGCTAGGAGCCGGAGGTGCTACGCGTACGTTTTTCCAGGGAACGGTTACGGTCGGTTCGGTGCGTTCGGAGGCGTCTCGTTCTACTCCACGAACTACGTGTGAATTAGGACAGTGAGCAGGGTCCTAGGGGCCAATGAGGGGGGTTCTGAGGCTACTGACTGAGCGGACCAAAGCAGGTCAGAAAGAGGCTCCTTGTGGGGGCTCAGGGCACAAAGGGAGCAACCGTGAGGGAACCTCGCGCGGTAGACTGCGCAATTGGGGGTCAGGTGCAAACCGCGGGCAGAAGGTGAGGGATACGACCAACCATAGCGCAGCAAGAGGCATAGTTTGTCTGGGCCGTGTAGTG--GTCTACCACGGGCCAGTACCCANTTTATGCAGCGGCCCCTTGTCCGCATGAGGAGCATCGATCGTCCTCCCATACCATTCAGCCCCGATTCATCGCAATCAGATTCTTCTGCCACAACTCCGATGT
->02_5877_MEX_TX_Fed_vcf
-ACCTTGTGCGCAGCCGGCATCATGTGACTACATGCGACCCACGTGGGACTCTTGACGACTCGGATCAGTCCAATGTACCCACCTCATGGTGTCAAAACTACGCGGCTAAGCTCAACCAAATTGGGCACGGTCCTCTAACATACCATGACTCGCCGTCTCGGAGGGTACAATAGTTCCCCATTGGCACGCGTCGCTCGCAGGGCACGTTTGTTGTTACTACCACCATTAATACTAAATTGGCACGTCCGAAGAGGCGTGGTAGGAGGTCGGCCACTCCATACCGTAAATGACTCTTTCGCAAGCAAACGGACTCATGCCTCACGCAGACTTAGCACATGGTCTACATACGTCCGTGCCAAGGAACGGTTGGTAATCTAACACACCGAAGAGAATTCTCCCTTGCGGGGAAAGACCTACGGAGCCCGTGGTGACAGACCATTCTCCGACTATTAGCAGAATGTACCTCAGAGGCGACATTGAGGTTAGCCAGAACAGAGCCAGCGGTATACGCCCAGGAATAGCTGAAGTCCGAGGCAGATGGTCACAGTAATCTTCAATCTAACGTGGTACATGGCCAGGGGCTGACCAGGGGCTTCAGGTGGGGAACGAAATGTGTACTGACTTGCGACACGGAGGAGAGCCCGACCCGGCCCAGTAACAAATGACCACCCGTAGACCGCTGCTATTTCCGGGACATGACACCTCTCCTCTAGTGCGCATACTATAAGGTAGTCCTTTGCAGCGCTCAGCTTGACCCCATTATATCACAGCGTCTTCACTCTGCGCTACGTCC
->root
-ATCTTTTGCGCAGCCGGCGCCGTGTGACTATGGGCGATCTACGTGAGACCCCTGGCGGCTCGGATCACTCCATTGTGCCCACTTCGTGGGGTCAAAACTACGCGGGTGACCTCAACCCGGTTGGCCGCGGTCCGCTAACACCCCATGACCCGCCGCTTCGGAGGGTACAGCAGTCGCTCATTAGCACGCGTCACCCGCAGGGTACATCCGTTGTTAACACCATCGCTAACACCAAATTGGCACCTCCGGGCAGGCCTCATCGGAGGTCGGCGGCCTCGCACCGCAGACGGCGCCCTCGCAAGCAACCGGACTCATGCGTCATACAGGCTTAGGACATGGTCTACATACGTCCGTGCCAAGCAATGGTTGGTAACTTAACACACCGGAGGGCATTCCCCCTGGCGCCGATAGACATGTGGAGCCCGTGGTGGCAGACCAGGTTCTGGCTGTCAACAAGGTGTATTCTGAAGCCGACATTGAAGTTAGCCAGAACCGAGTCAACGATGTACGCCCAGGAAGAGCTGAAGTCTAAGGCAAATGGTCACAGTAGAATCCAATCTAGCGTGGTACACGGCCGGGGGCTGACTAGGGGCTTCGGGTGGGGAGCGAAATGTGTGATGACTTACGGCGCGGAGAGAGGCCCGGCCCGGCTCAGTAACAAATGGTTGTCCGCAGCGCTCTGCCATTTCCTGGGCATGATACCTCTCCTCCAGTGCGCAGACCATAAGGCGGTTCCTTGCAGCGCTCAGCCTGAACCCATTATATCACAGCGCCGTTACTCTGCGCTACGCGC
diff -r 49aceeefab0a -r 2286f3a13e4d test-data/json_all_vcf2.json
--- a/test-data/json_all_vcf2.json	Fri Jun 18 18:12:16 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"columns":[
diff -r 49aceeefab0a -r 2286f3a13e4d test-data/json_avg_mq_all_vcf2.json
--- a/test-data/json_avg_mq_all_vcf2.json	Fri Jun 18 18:12:16 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"name":null,"index":
diff -r 49aceeefab0a -r 2286f3a13e4d vsnp_get_snps.xml
--- a/vsnp_get_snps.xml	Fri Jun 18 18:12:16 2021 +0000
+++ b/vsnp_get_snps.xml	Thu Jul 22 18:02:12 2021 +0000
@@ -1,12 +1,13 @@
-<tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@WRAPPER_VERSION@.1" profile="@PROFILE@">
+<tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@WRAPPER_VERSION@.0+galaxy0" profile="@PROFILE@">
     <description></description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.25.3">pandas</requirement>
+        <requirement type="package" version="3.0.7">openpyxl</requirement>
+        <requirement type="package" version="1.3.0">pandas</requirement>
         <requirement type="package" version="0.6.8">pyvcf</requirement>
-        <requirement type="package" version="1.2.0">xlrd</requirement>
+        <requirement type="package" version="2.0.1">xlrd</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #import re
@@ -109,6 +110,7 @@
                     <when value="cached">
                         <param name="input_excel" type="select" label="Excel file">
                             <options from_data_table="vsnp_excel">
+                                <filter type="data_meta" column="0" key="dbkey" ref="input_vcf_collection"/>
                                 <validator type="no_options" message="No built-in Excel grouping and filtering datasets are available"/>
                             </options>
                         </param>
@@ -184,10 +186,10 @@
                 <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/>
             </output_collection>
             <output_collection name="json_avg_mq" type="list" count="1">
-                <element name="all_vcf" file="json_avg_mq_all_vcf2.json" ftype="json" compare="contains"/>
+                <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/>
             </output_collection>
             <output_collection name="json_snps" type="list" count="1">
-                <element name="all_vcf" file="json_all_vcf2.json" ftype="json" compare="contains"/>
+                <element name="all_vcf" file="json_all_vcf.json" ftype="json" compare="contains"/>
             </output_collection>
             <output name="output_summary" file="output_summary2.html" ftype="html" compare="contains"/>
         </test>
@@ -241,7 +243,7 @@
             <param name="all_isolates" value="--all_isolates"/>
             <output_collection name="snps" type="list" count="2">
                 <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta"/>
-                <element name="all_vcf" file="all_vcf3.fasta" ftype="fasta"/>
+                <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/>
             </output_collection>
             <output_collection name="json_avg_mq" type="list" count="2">
                 <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/>