Mercurial > repos > iuc > tb_profiler_collate

comparison tb_profiler_collate.xml @ 1:e9568d48ee11 draft default tip

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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 10:24:50 +0000
parents 9fae5576604a
children
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0:9fae5576604a 1:e9568d48ee11
1 <tool id="tb_profiler_collate" name="TB-Profiler Collate" version="@TOOL_VERSION@@VERSION_SUFFIX@" profile="21.05"> 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> 2 <description>Combines multiple TB-Profiler JSON reports into summary and variants reports</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
15 #for $dataset in $input_files 15 #for $dataset in $input_files
16 python '$__tool_directory__/replace_id_field_with_element_id.py' '$dataset' '$dataset.element_identifier' && 16 python '$__tool_directory__/replace_id_field_with_element_id.py' '$dataset' '$dataset.element_identifier' &&
17 #end for 17 #end for
18 18
19 tb-profiler collate --dir . 19 tb-profiler collate --dir .
20
21 ]]></command> 20 ]]></command>
22 21
23 <inputs> 22 <inputs>
24 <param type="data_collection" name="input_files" label="TB-Profiler JSON Reports" collection_type="list" format="json" help="Enter a list of TB-Profiler JSON reports to collate."/> 23 <param type="data_collection" name="input_files" label="TB-Profiler JSON Reports" collection_type="list" format="json" help="Enter a list of TB-Profiler JSON reports to collate."/>
25 </inputs> 24 </inputs>
26 25
27 <outputs> 26 <outputs>
28 <data name="output_txt" format="txt" label="${tool.name} on ${on_string}: Summary Report" from_work_dir="tbprofiler.txt"/> 27 <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: Summary Report (tabular)" from_work_dir="tbprofiler.txt">
28 <actions>
29 <action name="column_names" type="metadata" default="sample,main_lineage,sub_lineage,spoligotype,drtype,target_median_depth,pct_reads_mapped,num_reads_mapped,num_dr_variants,num_other_variants,rifampicin,isoniazid,ethambutol,pyrazinamide,moxifloxacin,levofloxacin,bedaquiline,delamanid,pretomanid,linezolid,streptomycin,amikacin,kanamycin,capreomycin,clofazimine,ethionamide,para-aminosalicylic_acid,cycloserine"/>
30 <action type="metadata" name="detect_metadata"/>
31 </actions>
32 </data>
29 <data name="output_csv" format="csv" label="${tool.name} on ${on_string}: Variants Report (CSV)" from_work_dir="tbprofiler.variants.csv"/> 33 <data name="output_csv" format="csv" label="${tool.name} on ${on_string}: Variants Report (CSV)" from_work_dir="tbprofiler.variants.csv"/>
30 <data name="output_variants" format="txt" label="${tool.name} on ${on_string}: Variants Report (TXT)" from_work_dir="tbprofiler.variants.txt"/> 34 <data name="output_variants" format="txt" label="${tool.name} on ${on_string}: Variants Report (TXT)" from_work_dir="tbprofiler.variants.txt"/>
31 </outputs> 35 </outputs>
32 36
33 <tests> 37 <tests>
36 <collection type="list"> 40 <collection type="list">
37 <element name="ERR2510682" value="ERR2510682.results.json" ftype="json"/> 41 <element name="ERR2510682" value="ERR2510682.results.json" ftype="json"/>
38 </collection> 42 </collection>
39 </param> 43 </param>
40 44
41 <output name="output_txt" file="tbprofiler_test_1_sample.txt"/> 45 <output name="output_tabular" file="tbprofiler_test_1_sample.txt" ftype="tabular"/>
42 <output name="output_csv" file="tbprofiler_test_1_sample.variants.csv"/> 46 <output name="output_csv" file="tbprofiler_test_1_sample.variants.csv"/>
43 <output name="output_variants" file="tbprofiler_test_1_sample.variants.txt"/> 47 <output name="output_variants" file="tbprofiler_test_1_sample.variants.txt"/>
44 </test> 48 </test>
45 </tests> 49 </tests>
46 50