| Previous changeset 4:b08ac10aed96 (2021-06-07) Next changeset 6:79450f7fd718 (2022-08-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 004793bd31d2b4dcc065fb1fe3ad40fa98190c56 |
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modified:
est-abundance.xml macros.xml |
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added:
test-data/NC_011750.1_simulated_kraken_style_bracken_report.txt |
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| diff -r b08ac10aed96 -r 19035a7b1106 est-abundance.xml --- a/est-abundance.xml Mon Jun 07 20:32:37 2021 +0000 +++ b/est-abundance.xml Wed Jul 06 14:47:54 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy0"> +<tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Bayesian Reestimation of Abundance with KrakEN</description> <macros> <import>macros.xml</import> @@ -10,6 +10,9 @@ <edam_operations> <edam_operation>operation_2238</edam_operation> </edam_operations> + <xrefs> + <xref type="bio.tools">bracken</xref> + </xrefs> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ est_abundance.py @@ -18,6 +21,8 @@ -l $level -t $threshold -o '$report' + ## --out-report needs to be set always, since it is written next to the input file + --out-report bracken.report ]]> </command> <inputs> @@ -39,22 +44,28 @@ <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag" help="Threshold for the minimum number of reads kraken must assign to a classification for that classification to be considered in the final abundance estimation." /> + <param argument="--out-report" type="boolean" checked="false" label="Produce Kraken-Style Bracken report"/> </inputs> <outputs> <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" /> + <data name="kraken_report" format="tabular" from_work_dir="bracken.report" label="${tool.name} on ${on_string}: Kraken style report"> + <filter>out_report</filter> + </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/> <param name="level" value="S" /> <param name="bracken_database" value="test_entry"/> <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/> </test> - <test> + <test expect_num_outputs="2"> <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/> <param name="level" value="S" /> <param name="bracken_database" value="test_entry"/> + <param name="out_report" value="true"/> <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/> + <output name="kraken_report" file="NC_011750.1_simulated_kraken_style_bracken_report.txt" ftype="tabular"/> </test> </tests> <help> |
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| diff -r b08ac10aed96 -r 19035a7b1106 macros.xml --- a/macros.xml Mon Jun 07 20:32:37 2021 +0000 +++ b/macros.xml Wed Jul 06 14:47:54 2022 +0000 |
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| @@ -1,5 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">2.6.1</token> + <token name="@TOOL_VERSION@">2.7</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bracken</requirement> |
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| diff -r b08ac10aed96 -r 19035a7b1106 test-data/NC_011750.1_simulated_kraken_style_bracken_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_011750.1_simulated_kraken_style_bracken_report.txt Wed Jul 06 14:47:54 2022 +0000 |
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| @@ -0,0 +1,9 @@ +100.00 43 0 R 1 root +100.00 43 0 R1 131567 cellular organisms +100.00 43 0 D 2 Bacteria +100.00 43 0 P 1224 Proteobacteria +100.00 43 0 C 1236 Gammaproteobacteria +100.00 43 0 O 91347 Enterobacterales +100.00 43 0 F 543 Enterobacteriaceae +100.00 43 0 G 561 Escherichia +100.00 43 43 S 562 Escherichia coli |