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comparison adjust_bracken_for_unclassified_reads.xml @ 0:3ab9d37e547e draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 0d1d1f356cdfd8ef6dbcdd1bfe76c4637587ff53"
author public-health-bioinformatics
date Thu, 10 Mar 2022 21:35:14 +0000
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children 3cde438eb222
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-1:000000000000 0:3ab9d37e547e
1 <tool id="adjust_bracken_for_unclassified_reads" name="Adjust Bracken Report for Unclassified Reads" version="0.1.0">
2 <description>Adjust bracken report to account for unclassified reads</description>
3 <requirements>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 '$__tool_directory__/adjust_bracken_for_unclassified_reads.py'
7 --kraken-report '${kraken_report}'
8 --bracken-abundances '${bracken_abundances}'
9 > ${adjusted_bracken_report}
10 ]]></command>
11 <inputs>
12 <param name="kraken_report" type="data" format="txt" />
13 <param name="bracken_abundances" type="data" format="txt" />
14 </inputs>
15 <outputs>
16 <data name="adjusted_bracken_report" label="Adjusted Report" format="txt"/>
17 </outputs>
18 <tests>
19 <test>
20 <param name="kraken_report" value="input/SRR17619849_kraken2.txt"/>
21 <param name="bracken_abundances" value="input/SRR17619849_bracken_abundances.tsv"/>
22 <output name="adjusted_bracken_report" file="output/SRR17619849_bracken_abundances_adjusted.tsv" ftype="tabular"/>
23 </test>
24 <test>
25 <param name="kraken_report" value="input/SRR17907745_kraken2.txt"/>
26 <param name="bracken_abundances" value="input/SRR17907745_bracken_abundances.tsv"/>
27 <output name="adjusted_bracken_report" file="output/SRR17907745_bracken_abundances_adjusted.tsv" ftype="tabular"/>
28 </test>
29 </tests>
30 <help><![CDATA[
31 ]]></help>
32 <citations>
33 </citations>
34 </tool>