Mercurial > repos > iuc > tb_profiler_collate

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