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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler commit 7dba70c70c9fe33353a0fd21803b11cfddc42c32
author iuc
date Tue, 21 Oct 2025 10:24:27 +0000
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1 <tool id="tb_profiler_collate" name="TB-Profiler Collate" version="@TOOL_VERSION@+galaxy1" profile="21.05">
2 <description>Combines multiple TB-Profiler JSON reports into summary and variants reports</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
10 </requirements>
11
12 <expand macro="version_command"/>
13
14 <command detect_errors="exit_code"><![CDATA[
15 #for $dataset in $input_files
16 python '$__tool_directory__/replace_id_field_with_element_id.py' '$dataset' '$dataset.element_identifier' &&
17 #end for
18
19 tb-profiler collate --dir .
20 ]]></command>
21
22 <inputs>
23 <param type="data_collection" name="input_files" label="TB-Profiler JSON Reports" collection_type="list" format="json" help="Enter a list of TB-Profiler JSON reports to collate."/>
24 </inputs>
25
26 <outputs>
27 <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: Summary Report (tabular)" from_work_dir="tbprofiler.txt">
28 <actions>
29 <action name="column_names" type="metadata" default="sample,main_lineage,sub_lineage,spoligotype,drtype,target_median_depth,pct_reads_mapped,num_reads_mapped,num_dr_variants,num_other_variants,rifampicin,isoniazid,ethambutol,pyrazinamide,moxifloxacin,levofloxacin,bedaquiline,delamanid,pretomanid,linezolid,streptomycin,amikacin,kanamycin,capreomycin,clofazimine,ethionamide,para-aminosalicylic_acid,cycloserine"/>
30 <action type="metadata" name="detect_metadata"/>
31 </actions>
32 </data>
33 <data name="output_csv" format="csv" label="${tool.name} on ${on_string}: Variants Report (CSV)" from_work_dir="tbprofiler.variants.csv"/>
34 <data name="output_variants" format="txt" label="${tool.name} on ${on_string}: Variants Report (TXT)" from_work_dir="tbprofiler.variants.txt"/>
35 </outputs>
36
37 <tests>
38 <test expect_num_outputs="3">
39 <param name="input_files">
40 <collection type="list">
41 <element name="ERR2510682" value="ERR2510682.results.json" ftype="json"/>
42 </collection>
43 </param>
44
45 <output name="output_tabular" file="tbprofiler_test_1_sample.txt" ftype="tabular"/>
46 <output name="output_csv" file="tbprofiler_test_1_sample.variants.csv"/>
47 <output name="output_variants" file="tbprofiler_test_1_sample.variants.txt"/>
48 </test>
49 </tests>
50
51 <help><![CDATA[
52 TB-Profiler Collate Tool
53
54 This tool combines multiple TB-Profiler JSON reports into consolidated outputs, summarizing lineage, antimicrobial resistance (AMR) profiles, and variants across samples.
55
56 Inputs
57 - A collection of TB-Profiler JSON reports generated from individual samples.
58
59 Outputs
60 1. Summary Report (tbprofiler.txt): Overview of sample lineages and AMR predictions.
61 2. Variants CSV (tbprofiler.variants.csv): Table of identified variants across all samples.
62 3. Variants Text (tbprofiler.variants.txt): Text file of variant details for quick inspection.
63
64 Usage Notes
65 - Ensure all input JSON files are valid TB-Profiler outputs.
66
67 ]]></help>
68
69 <citations>
70 <citation type="doi">10.1186/s13073-019-0676-5</citation>
71 </citations>
72
73 </tool>