| Previous changeset 5:19035a7b1106 (2022-07-06) Next changeset 7:978ae4147c29 (2023-05-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649 |
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modified:
est-abundance.xml macros.xml |
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added:
test-data/NC_003198.1_simulated_kraken_style_bracken_report.txt test-data/test2.log |
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| diff -r 19035a7b1106 -r 79450f7fd718 est-abundance.xml --- a/est-abundance.xml Wed Jul 06 14:47:54 2022 +0000 +++ b/est-abundance.xml Fri Aug 26 07:21:39 2022 +0000 |
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| @@ -1,30 +1,25 @@ -<tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>Bayesian Reestimation of Abundance with KrakEN</description> +<tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Bayesian Reestimation of Abundance with Kraken</description> <macros> <import>macros.xml</import> </macros> - <edam_topics> - <edam_topic>topic_3174</edam_topic> - <edam_topic>topic_3697</edam_topic> - </edam_topics> - <edam_operations> - <edam_operation>operation_2238</edam_operation> - </edam_operations> - <xrefs> - <xref type="bio.tools">bracken</xref> - </xrefs> - <expand macro="requirements" /> + <expand macro="edam" /> + <expand macro="xref" /> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - est_abundance.py - -i '$input' - -k '$kmer_distr.fields.path' - -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 + est_abundance.py + -i '$input' + -k '$kmer_distr.fields.path' + -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 + #if $logfile_output == "True" + | tee '$logfile' + #end if ]]> - </command> + </command> <inputs> <param name="input" type="data" format="tabular" label="Kraken report file" /> <param label="Select a Kmer distribution" name="kmer_distr" type="select"> @@ -42,35 +37,42 @@ <option value="D">Domain</option> </param> <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 + 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"/> + <param name="logfile_output" type="boolean" truevalue="True" falsevalue="False" label="Add log file output"/> </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 ${on_string}: Kraken style report"> <filter>out_report</filter> </data> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"> + <filter> logfile_output == True </filter> + </data> </outputs> <tests> <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"/> + <param name="kmer_distr" value="test_entry"/> + <param name="logfile_output" value="False"/> <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/> </test> - <test expect_num_outputs="2"> + <test expect_num_outputs="3"> <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="kmer_distr" value="test_entry"/> <param name="out_report" value="true"/> + <param name="logfile_output" 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"/> + <output name="logfile" file="test2.log" lines_diff="8" /> </test> </tests> <help> <![CDATA[ - Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_. + Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>` ]]></help> <expand macro="citations" /> </tool> |
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| diff -r 19035a7b1106 -r 79450f7fd718 macros.xml --- a/macros.xml Wed Jul 06 14:47:54 2022 +0000 +++ b/macros.xml Fri Aug 26 07:21:39 2022 +0000 |
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| @@ -1,6 +1,7 @@ <macros> <token name="@TOOL_VERSION@">2.7</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@PROFILE@">21.05</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bracken</requirement> @@ -9,6 +10,20 @@ <xml name="version"> <version_command>echo @TOOL_VERSION@</version_command> </xml> + <xml name="edam"> + <edam_topics> + <edam_topic>topic_3174</edam_topic> + <edam_topic>topic_3697</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_2238</edam_operation> + </edam_operations> + </xml> + <xml name="xref"> + <xrefs> + <xref type="bio.tools">bracken</xref> + </xrefs> + </xml> <xml name="citations"> <citations> <citation type="doi">10.7717/peerj-cs.104</citation> |
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| diff -r 19035a7b1106 -r 79450f7fd718 test-data/NC_003198.1_simulated_kraken_style_bracken_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_simulated_kraken_style_bracken_report.txt Fri Aug 26 07:21:39 2022 +0000 |
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| @@ -0,0 +1,9 @@ +100.00 42 0 R 1 root +100.00 42 0 R1 131567 cellular organisms +100.00 42 0 D 2 Bacteria +100.00 42 0 P 1224 Proteobacteria +100.00 42 0 C 1236 Gammaproteobacteria +100.00 42 0 O 91347 Enterobacterales +100.00 42 0 F 543 Enterobacteriaceae +100.00 42 0 G 590 Salmonella +100.00 42 42 S 28901 Salmonella enterica |
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| diff -r 19035a7b1106 -r 79450f7fd718 test-data/test2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.log Fri Aug 26 07:21:39 2022 +0000 |
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| @@ -0,0 +1,14 @@ +PROGRAM START TIME: 08-05-2022 14:41:48 +BRACKEN SUMMARY (Kraken report: /tmp/tmpy56dgetr/files/f/5/4/dataset_f5412c50-3888-4466-b041-32814cdda47c.dat) + >>> Threshold: 10 + >>> Number of species in sample: 1 + >> Number of species with reads > threshold: 1 + >> Number of species with reads < threshold: 0 + >>> Total reads in sample: 45 + >> Total reads kept at species level (reads > threshold): 42 + >> Total reads discarded (species reads < threshold): 0 + >> Reads distributed: 1 + >> Reads not distributed (eg. no species above threshold): 0 + >> Unclassified reads: 2 +BRACKEN OUTPUT PRODUCED: /tmp/tmpy56dgetr/job_working_directory/000/4/outputs/galaxy_dataset_e099cc44-07e6-4507-b11f-137722113078.dat +PROGRAM END TIME: 08-05-2022 14:41:48 |