Mercurial > repos > iuc > tb_profiler_collate

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit a6f87bb33981b0fc0c9b7a9dd822259d9a29a3a1
author iuc
date Fri, 05 Sep 2025 12:50:05 +0000
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9fae5576604a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit a6f87bb33981b0fc0c9b7a9dd822259d9a29a3a1
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1 <tool id="tb_profiler_collate" name="TB-Profiler Collate" version="@TOOL_VERSION@@VERSION_SUFFIX@" 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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21 ]]></command>
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23 <inputs>
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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."/>
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25 </inputs>
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27 <outputs>
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28 <data name="output_txt" format="txt" label="${tool.name} on ${on_string}: Summary Report" from_work_dir="tbprofiler.txt"/>
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29 <data name="output_csv" format="csv" label="${tool.name} on ${on_string}: Variants Report (CSV)" from_work_dir="tbprofiler.variants.csv"/>
9fae5576604a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit a6f87bb33981b0fc0c9b7a9dd822259d9a29a3a1
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30 <data name="output_variants" format="txt" label="${tool.name} on ${on_string}: Variants Report (TXT)" from_work_dir="tbprofiler.variants.txt"/>
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31 </outputs>
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33 <tests>
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34 <test expect_num_outputs="3">
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35 <param name="input_files">
9fae5576604a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit a6f87bb33981b0fc0c9b7a9dd822259d9a29a3a1
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36 <collection type="list">
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37 <element name="ERR2510682" value="ERR2510682.results.json" ftype="json"/>
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38 </collection>
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39 </param>
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41 <output name="output_txt" file="tbprofiler_test_1_sample.txt"/>
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42 <output name="output_csv" file="tbprofiler_test_1_sample.variants.csv"/>
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43 <output name="output_variants" file="tbprofiler_test_1_sample.variants.txt"/>
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44 </test>
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45 </tests>
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47 <help><![CDATA[
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48 TB-Profiler Collate Tool
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50 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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52 Inputs
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53 - A collection of TB-Profiler JSON reports generated from individual samples.
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54
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55 Outputs
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56 1. Summary Report (tbprofiler.txt): Overview of sample lineages and AMR predictions.
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57 2. Variants CSV (tbprofiler.variants.csv): Table of identified variants across all samples.
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58 3. Variants Text (tbprofiler.variants.txt): Text file of variant details for quick inspection.
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59
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60 Usage Notes
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61 - Ensure all input JSON files are valid TB-Profiler outputs.
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62
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63 ]]></help>
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65 <citations>
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66 <citation type="doi">10.1186/s13073-019-0676-5</citation>
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67 </citations>
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69 </tool>