Mercurial > repos > iuc > tbprofiler

annotate tb_profiler_profile.xml @ 8:037a11682176 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 2f5daa493f383fc92cf20a45b6049da4d31c70e5"
author iuc
date Wed, 06 Jan 2021 14:42:20 +0000
parents 200c378d85f3
children e1a9d6fd258d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy1">
2
49b819f88c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
iuc
parents: 1
diff changeset
2 <description>Infer strain types and drug resistance markers from sequences</description>
3
19793eecc9f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 5679ad1f1d5cac6c6168ad91dd4ca3616d22ca35"
iuc
parents: 2
diff changeset
3 <macros>
19793eecc9f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 5679ad1f1d5cac6c6168ad91dd4ca3616d22ca35"
iuc
parents: 2
diff changeset
4 <import>macros.xml</import>
19793eecc9f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 5679ad1f1d5cac6c6168ad91dd4ca3616d22ca35"
iuc
parents: 2
diff changeset
5 </macros>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
6 <requirements>
3
19793eecc9f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 5679ad1f1d5cac6c6168ad91dd4ca3616d22ca35"
iuc
parents: 2
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
8 </requirements>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
10 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
11 #if str($fastq_or_bam.input_select.value) == "paired_fastq"
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
12 #set r1_ext = $fastq_or_bam.read1.extension
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
13 #set r2_ext = $fastq_or_bam.read2.extension
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
14 ln -s '$fastq_or_bam.read1' fastq_r1.'$r1_ext' &&
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
15 ln -s '$fastq_or_bam.read2' fastq_r2.'$r2_ext' &&
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
16 #else if str($fastq_or_bam.input_select.value) == "single_fastq"
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
17 #set r1_ext = $fastq_or_bam.fastq.extension
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
18 ln -s '$fastq_or_bam.fastq' fastq_r1.'$r1_ext' &&
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
19 #else if str($fastq_or_bam.input_select.value) == "paired_collection_fastq"
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
20 #set r1_ext = $fastq_or_bam.fastq_collection.forward.extension
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
21 #set r2_ext = $fastq_or_bam.fastq_collection.reverse.extension
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
22 ln -s '$fastq_or_bam.fastq_collection.forward' fastq_r1.'$r1_ext' &&
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
23 ln -s '$fastq_or_bam.fastq_collection.reverse' fastq_r2.'$r2_ext' &&
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
24 #end if
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
25 #else if str($fastq_or_bam.input_select.value) == "bam"
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
26 ln -s '$fastq_or_bam.bam_input' input.bam &&
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
27 #end if
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
28
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
29 tb-profiler profile
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
30
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
31 --platform '${platform.value}'
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
32
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
33 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
34 -1 fastq_r1.'$r1_ext'
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
35 #end if
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
36 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq")
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
37 -2 fastq_r2.'$r1_ext'
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
38 #else if str($fastq_or_bam.input_select.value) == "bam"
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
39 --bam input.bam
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
40 #end if
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
41
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
42 --threads "\${GALAXY_SLOTS:-1}"
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
43 #if $advanced.options == 'yes'
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
44 --mapper '${advanced.mapper}'
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
45 --min_depth '${advanced.min_depth}'
7
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
46 --af '${advanced.min_allele_freq}'
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
47 --reporting_af '${advanced.min_allele_freq_reporting}'
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
48 #end if
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
49
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
50 #if $output_format == "pdf"
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
51 --pdf
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
52 #else if $output_format == "txt"
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
53 --txt
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
54 #end if
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
55 && mv results/tbprofiler.results.json $results_json
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
56 #if str($fastq_or_bam.input_select) != "bam"
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
57 && mv bam/tbprofiler.bam '${output_bam}'
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
58 #end if
4
c2656b729ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit a51548708ea975c0a7b135a2cbaa5d094f3c5602"
iuc
parents: 3
diff changeset
59 && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.csq.vcf.gz
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
60 #if $output_format == "pdf"
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
61 && mv results/tbprofiler.results.pdf '${output_pdf}'
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
62 #else if $output_format == "txt"
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
63 && mv results/tbprofiler.results.txt '${output_txt}'
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
64 #end if
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
65
2
49b819f88c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
iuc
parents: 1
diff changeset
66 ]]> </command>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
67 <inputs>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
68 <param name="platform" type="select" label="Platform">
5
4272bd430a01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 4ad0b10ff7acfadf4cc0a6befa430274b8c47135"
iuc
parents: 4
diff changeset
69 <option value="illumina" selected="true">Illumina</option>
4272bd430a01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 4ad0b10ff7acfadf4cc0a6befa430274b8c47135"
iuc
parents: 4
diff changeset
70 <option value="nanopore">Nanopore</option>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
71 </param>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
72 <conditional name="fastq_or_bam">
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
73 <param name="input_select" type="select" label="Input File Type">
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
74 <option value="paired_fastq">Paired Fastq</option>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
75 <option value="paired_collection_fastq">Paired Collection Fastq</option>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
76 <option value="single_fastq">Single Fastq</option>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
77 <option value="bam">BAM</option>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
78 </param>
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
79 <when value="paired_fastq">
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
80 <param name="read1" type="data" format="fastq" label="Read1" help="First read file (default: None)"/>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
81 <param name="read2" type="data" format="fastq" optional="true" label="Read2" help="Second read file (default: None)"/>
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
82 </when>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
83 <when value="paired_collection_fastq">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
84 <param label="Reads (collection)" name="fastq_collection" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
85 </when>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
86 <when value="single_fastq">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
87 <param label="Reads" name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
2
49b819f88c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
iuc
parents: 1
diff changeset
88 </when>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
89 <when value="bam">
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
90 <param name="bam_input" type="data" format="bam" label="Bam" help="Warning!!!: The BAM files must have been created using the ensembl version of the genome."/>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
91 </when>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
92 </conditional>
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
93 <param name="output_format" label="Output format" type="select">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
94 <option value="txt">Text</option>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
95 <option value="pdf">PDF</option>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
96 </param>
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
97 <conditional name="advanced">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
98 <param label="Select advanced options" type="select" name="options">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
99 <option value="yes">Yes</option>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
100 <option value="no" selected="true">No</option>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
101 </param>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
102 <when value="no">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
103 </when>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
104 <when value="yes">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
105 <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
106 <option value="bwa" selected="true">bwa</option>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
107 <option value="minimap2">minimap2</option>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
108 <option value="bowtie2">bowtie2</option>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
109 </param>
7
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
110 <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
111 <param name="min_allele_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)" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
112 <param name="min_allele_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)"/>
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
113 </when>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
114 </conditional>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
115 </inputs>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
116 <outputs>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
117 <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
118 <data format="vcf" name="output_vcf" label="${tool.name} VCF on ${on_string}" />
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
119 <data format="bam" name="output_bam" label="${tool.name} BAM on ${on_string}">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
120 <filter>fastq_or_bam['input_select'] != 'bam'</filter>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
121 </data>
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
122 <data format="pdf" name="output_pdf" label="${tool.name} PDF report on ${on_string}">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
123 <filter>output_format == 'pdf'</filter>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
124 </data>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
125 <data format="txt" name="output_txt" label="${tool.name} report on ${on_string}">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
126 <filter>output_format == 'txt'</filter>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
127 </data>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
128
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
129 </outputs>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
130 <tests>
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
131 <test>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
132 <param name="input_select" value="single_fastq"/>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
133 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
134 <param name="output_format" value="txt" />
5
4272bd430a01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 4ad0b10ff7acfadf4cc0a6befa430274b8c47135"
iuc
parents: 4
diff changeset
135 <param name="platform" value="illumina" />
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
136 <param name="options" value="no" />
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
137 <output name="output_txt">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
138 <assert_contents>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
139 <has_line line="Drug-resistance: Drug-resistant" />
2
49b819f88c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
iuc
parents: 1
diff changeset
140 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
49b819f88c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
iuc
parents: 1
diff changeset
141 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
49b819f88c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
iuc
parents: 1
diff changeset
142 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
143 </assert_contents>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
144 </output>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
145 </test>
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
146 <test>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
147 <param name="input_select" value="bam"/>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
148 <param name="bam_input" ftype="bam" value="rif_resistant.bam" />
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
149 <param name="output_format" value="txt" />
5
4272bd430a01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 4ad0b10ff7acfadf4cc0a6befa430274b8c47135"
iuc
parents: 4
diff changeset
150 <param name="platform" value="illumina" />
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
151 <param name="options" value="no" />
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
152 <output name="output_txt">
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
153 <assert_contents>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
154 <has_line line="Drug-resistance: Drug-resistant" />
2
49b819f88c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
iuc
parents: 1
diff changeset
155 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
49b819f88c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
iuc
parents: 1
diff changeset
156 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
49b819f88c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
iuc
parents: 1
diff changeset
157 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
158 </assert_contents>
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
iuc
parents: 0
diff changeset
159 </output>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
160 </test>
7
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
161 <test>
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
162 <param name="input_select" value="single_fastq"/>
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
163 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
164 <param name="output_format" value="txt" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
165 <param name="platform" value="illumina" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
166 <param name="options" value="yes" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
167 <param name="call_whole_genome" value="true" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
168 <param name="min_allele_freq" value="0.25" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
169 <param name="min_allele_freq_reporting" value="0.33" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
170 <output name="output_txt">
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
171 <assert_contents>
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
172 <has_line line="Drug-resistance: Drug-resistant" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
173 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
174 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
175 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
176 </assert_contents>
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
177 </output>
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
iuc
parents: 5
diff changeset
178 </test>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
179 </tests>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
180 <help><![CDATA[
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
181 Summary
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
182 =======
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
183
4
c2656b729ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit a51548708ea975c0a7b135a2cbaa5d094f3c5602"
iuc
parents: 3
diff changeset
184 The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using GATK. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data).
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
185
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
186 Produces a JSON output file by default.
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
187
2
49b819f88c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
iuc
parents: 1
diff changeset
188 ]]> </help>
0
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
189 <citations>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
190 <citation type="bibtex">
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
191 @UNPUBLISHED{Phelan2016,
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
192 author = {Phelan, Jody},
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
193 title = {TBProfiler},
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
194 year = {2016},
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
195 url = {https://github.com/jodyphelan/TBProfiler},
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
196 }
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
197 </citation>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
198 </citations>
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
199 </tool>