# HG changeset patch
# User iuc
# Date 1565987191 14400
# Node ID 19793eecc9f0e33c5b21de2c66438793d3f409c8
# Parent  49b819f88c2b7aa5e84f70a70a2ba1d7ca9f8c1e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 5679ad1f1d5cac6c6168ad91dd4ca3616d22ca35"

diff -r 49b819f88c2b -r 19793eecc9f0 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Aug 16 16:26:31 2019 -0400
@@ -0,0 +1,3 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.6</token>
+</macros>
diff -r 49b819f88c2b -r 19793eecc9f0 tb_profiler_profile.xml
--- a/tb_profiler_profile.xml	Tue Jul 16 08:29:18 2019 -0400
+++ b/tb_profiler_profile.xml	Fri Aug 16 16:26:31 2019 -0400
@@ -1,7 +1,10 @@
-<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.4">
+<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0">
     <description>Infer strain types and drug resistance markers from sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="2.4">tb-profiler</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
@@ -42,6 +45,8 @@
             --min_gene_frac '${advanced.min_gene_frac}'
             --mapper '${advanced.mapper}'
             --min_depth '${advanced.min_depth}'
+            --af '${min_allel_freq}'
+            --reporting_af '${min_allel_freq_reporting}'
         #end if
 
         #if $output_format == "pdf"
@@ -113,6 +118,8 @@
                     <option value="bowtie2">bowtie2</option>
                 </param>
                 <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)" />
+                <param name="min_allel_freq" argument="--af" type="float" value="0.1" label="Minimum allele frequency to call variants" help=" Minimum allele frequency to call variants (default: 0.1)" />
+                <param name="min_allel_freq_reporting" argument="--reporting_af" value="0.1" label="Reporting Minimum allele frequency to call variants" type="float" help=" Minimum allele frequency to call variants (default: 0.1)"/>
             </when>
         </conditional>
     </inputs>
diff -r 49b819f88c2b -r 19793eecc9f0 test-data/example.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.vcf	Fri Aug 16 16:26:31 2019 -0400
@@ -0,0 +1,18 @@
+##fileformat=VCFv4.0
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele Count">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Number of Alleles With Data">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	X1	X2	X3	X4	X5	X6
+1	10	1:10	A	T	100	PASS	NS=5;AC=0;AN=10;AF=0.000000	GT	0/0	./.	0/0	0/0	0/0	0/0
+1	20	1:20	G	C	100	PASS	NS=0;AC=0;AN=0	GT	./.	./.	./.	./.	./.	./.
+1	30	1:30	C	A	100	PASS	NS=6;AC=0;AN=12;AF=0.000000	GT	0/0	0/0	0/0	0/0	0/0	0/0
+1	40	1:40	A	C	100	PASS	NS=6;AC=0;AN=12;AF=0.000000	GT	0/0	0/0	0/0	0/0	0/0	0/0
+1	10000	1:10000	G	C	100	PASS	NS=6;AC=0;AN=12;AF=0.000000	GT	0/0	0/0	0/0	0/0	0/0	0/0
+1	20000	1:20000	T	A	100	PASS	NS=6;AC=12;AN=12;AF=1.000000	GT	1/1	1/1	1/1	1/1	1/1	1/1
+4	5000	4:5000	A	T	100	PASS	NS=6;AC=12;AN=12;AF=1.000000	GT	1/1	1/1	1/1	1/1	1/1	1/1
+4	6000	4:6000	C	T	100	PASS	NS=6;AC=11;AN=12;AF=0.916667	GT	1/1	1/1	1/1	1/1	0/1	1/1
+X	800	X:800	A	C	100	PASS	NS=6;AC=12;AN=12;AF=1.000000	GT	1/1	1/1	1/1	1/1	1/1	1/1
+X	900	X:900	A	T	100	PASS	NS=6;AC=12;AN=12;AF=1.000000	GT	1/1	1/1	1/1	1/1	1/1	1/1
+X	1000	X:1000	T	G	100	PASS	NS=5;AC=10;AN=10;AF=1.000000	GT	1/1	1/1	1/1	1/1	1/1	./.
diff -r 49b819f88c2b -r 19793eecc9f0 test-data/example.vcf.gz
Binary file test-data/example.vcf.gz has changed
diff -r 49b819f88c2b -r 19793eecc9f0 test-data/rif_resistant.bam
Binary file test-data/rif_resistant.bam has changed