| Previous changeset 5:6c09bed3444f (2018-09-13) Next changeset 7:1c677354ab18 (2024-03-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8" |
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modified:
kraken-report.xml macros.xml tool-data/kraken_databases.loc.sample |
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added:
test-data/kraken-report/kraken_mpa_report_input1.tab test-data/kraken-report/kraken_mpa_report_input2.tab test-data/kraken-report/kraken_mpa_report_test1_output.tab test-data/kraken-report/kraken_report_test1.tab test-data/kraken-report/kraken_report_test1_output.tab test-data/kraken-report/test_database.loc |
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removed:
kraken-mpa-report.xml test-data/kraken_mpa_report_input1.tab test-data/kraken_mpa_report_input2.tab test-data/kraken_mpa_report_test1_output.tab test-data/kraken_report_test1.tab test-data/kraken_report_test1_output.tab test-data/test_database.loc test-data/test_db/database.idx test-data/test_db/database.kdb test-data/test_db/taxonomy/names.dmp test-data/test_db/taxonomy/nodes.dmp |
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| diff -r 6c09bed3444f -r 1902d3de4a4f kraken-mpa-report.xml --- a/kraken-mpa-report.xml Thu Sep 13 09:45:15 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,81 +0,0 @@ -<?xml version="1.0"?> -<tool id="kraken-mpa-report" name="Kraken-mpa-report" version="@WRAPPER_VERSION@"> - <description>view report of classification for multiple samples</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="version_command" /> - <command detect_errors="exit_code"><![CDATA[ - #set $names = [] - - #for $input_count, $input_classification in enumerate( $classification ): - #set $name_base = str( getattr( $input_classification, 'element_identifier', 'sample' ) ).replace( "/", '-' ).replace( "\t", "-" ) - #set $name = $name_base - #set $i = 1 - #while $name in $names: - #set $name = "%s_%s" % ( $name_base, $i ) - #set $i = $i + 1 - #end while - #silent $names.append( $name ) - ln -s '${input_classification}' '${name}' && - #end for - - @SET_DATABASE_PATH@ && - - kraken-mpa-report - @INPUT_DATABASE@ - #for $name in $names: - '${name}' - #end for - - ${show_zeros} - ${header_line} - - > '$output_report' - ]]></command> - <inputs> - <param name="classification" format="tabular" label="Kraken output" multiple="True" type="data" /> - <param name="show_zeros" argument="--show-zeros" type="boolean" falsevalue="" truevalue="--show-zeros" checked="False" - label="Display taxa even if they lack a read in any sample" /> - <param name="header_line" argument="--header-line" type="boolean" truevalue="--header-line" falsevalue="" checked="False" - label="Display a header line indicating sample IDs"/> - - <expand macro="input_database" /> - </inputs> - <outputs> - <data format="tabular" name="output_report" /> - </outputs> - <tests> - <test> - <param name="classification" value="kraken_mpa_report_input1.tab,kraken_mpa_report_input2.tab" ftype="tabular"/> - <param name="show_zeros" value="--show-zeros"/> - <param name="header_line" value="--header-line"/> - <param name="kraken_database" value="test_db"/> - - <output name="output_report" ftype="tabular" file="kraken_mpa_report_test1_output.tab" /> - </test> - </tests> - <help> -<![CDATA[ - -.. class:: warningmark - -**Note**: the database used must be the same as the one used in the original Kraken run - ------ - -**What is Does** - -Kraken-mpa-report summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple experiments, conditions, locations, etc. - ------ - -**Output** - -The output of kraken-mpa-report is a tab-delimited table, with one line per taxon. - -]]> - </help> - <expand macro="citations" /> -</tool> |
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| diff -r 6c09bed3444f -r 1902d3de4a4f kraken-report.xml --- a/kraken-report.xml Thu Sep 13 09:45:15 2018 -0400 +++ b/kraken-report.xml Wed Dec 04 06:52:03 2019 -0500 |
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| @@ -24,9 +24,9 @@ </outputs> <tests> <test> - <param name="kraken_output" value="kraken_report_test1.tab" ftype="tabular"/> - <param name="kraken_database" value="test_db"/> - <output name="output_report" ftype="tabular" file="kraken_report_test1_output.tab"/> + <param name="kraken_output" value="kraken-report/kraken_report_test1.tab" ftype="tabular"/> + <param name="kraken_database" value="new_style_test_entry"/> + <output name="output_report" ftype="tabular" file="kraken-report/kraken_report_test1_output.tab"/> </test> </tests> |
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| diff -r 6c09bed3444f -r 1902d3de4a4f macros.xml --- a/macros.xml Thu Sep 13 09:45:15 2018 -0400 +++ b/macros.xml Wed Dec 04 06:52:03 2019 -0500 |
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| @@ -1,9 +1,9 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">1.2.4</token> + <token name="@WRAPPER_VERSION@">1.3.1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement> + <requirement type="package" version="1.1.1">kraken</requirement> </requirements> </xml> <xml name="version_command"> @@ -23,6 +23,10 @@ <citation type="doi">10.1186/gb-2014-15-3-r46</citation> </citations> </xml> - <token name="@INPUT_DATABASE@">--db '${kraken_database.fields.name}'</token> - <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH='${kraken_database.fields.path}'</token> + <!-- See the kraken_databases.loc.sample documentation, + this if statement is for backward compatibility as early + versions of the wrapper assumed the UI facing field name + was also part of the directory path --> + <token name="@SET_DATABASE_PATH@">if [ -d '${kraken_database.fields.path}/${kraken_database.fields.name}' ]; then export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}/${kraken_database.fields.name}'; else export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}'; fi</token> + <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token> </macros> |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/kraken-report/kraken_mpa_report_input1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken-report/kraken_mpa_report_input1.tab Wed Dec 04 06:52:03 2019 -0500 |
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| @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/kraken-report/kraken_mpa_report_input2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken-report/kraken_mpa_report_input2.tab Wed Dec 04 06:52:03 2019 -0500 |
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| @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/kraken-report/kraken_mpa_report_test1_output.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken-report/kraken_mpa_report_test1_output.tab Wed Dec 04 06:52:03 2019 -0500 |
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| @@ -0,0 +1,8 @@ +#Sample ID kraken_mpa_report_input1.tab kraken_mpa_report_input2.tab +d__Bacteria 4 4 +d__Bacteria|p__Proteobacteria 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli 4 4 |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/kraken-report/kraken_report_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken-report/kraken_report_test1.tab Wed Dec 04 06:52:03 2019 -0500 |
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| @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/kraken-report/kraken_report_test1_output.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken-report/kraken_report_test1_output.tab Wed Dec 04 06:52:03 2019 -0500 |
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| @@ -0,0 +1,11 @@ + 0.00 0 0 U 0 unclassified +100.00 4 0 - 1 root +100.00 4 0 - 131567 cellular organisms +100.00 4 0 D 2 Bacteria +100.00 4 0 P 1224 Proteobacteria +100.00 4 0 C 1236 Gammaproteobacteria +100.00 4 0 O 91347 Enterobacteriales +100.00 4 0 F 543 Enterobacteriaceae +100.00 4 0 G 561 Escherichia +100.00 4 0 S 562 Escherichia coli +100.00 4 4 - 83333 Escherichia coli K-12 |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/kraken-report/test_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken-report/test_database.loc Wed Dec 04 06:52:03 2019 -0500 |
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| @@ -0,0 +1,20 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (folder name containing the Kraken DB) +# +# Modern usage assumes $path is the folder containing +# the Kraken database of interest: +# +new_style_test_entry "Test Database" ${__HERE__}/test_db + +# The kraken wrapper still supports an alternative +# legacy usage where $path/$name is the folder +# containing the Kraken database of interest, meaning +# $name must be both a folder name and human readable +# description of the DB to show in the Galaxy UI: +old_style_test_entry test_db ${__HERE__} + +# NOTE: This legacy style should be avoided as other +# tools also using the kraken_database.loc file may +# not understand it! |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/kraken_mpa_report_input1.tab --- a/test-data/kraken_mpa_report_input1.tab Thu Sep 13 09:45:15 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 -C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 -C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 -C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/kraken_mpa_report_input2.tab --- a/test-data/kraken_mpa_report_input2.tab Thu Sep 13 09:45:15 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 -C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 -C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 -C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/kraken_mpa_report_test1_output.tab --- a/test-data/kraken_mpa_report_test1_output.tab Thu Sep 13 09:45:15 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -#Sample ID kraken_mpa_report_input1.tab kraken_mpa_report_input2.tab -d__Bacteria 4 4 -d__Bacteria|p__Proteobacteria 4 4 -d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 4 4 -d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales 4 4 -d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae 4 4 -d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia 4 4 -d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli 4 4 |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/kraken_report_test1.tab --- a/test-data/kraken_report_test1.tab Thu Sep 13 09:45:15 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 -C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 -C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 -C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/kraken_report_test1_output.tab --- a/test-data/kraken_report_test1_output.tab Thu Sep 13 09:45:15 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,11 +0,0 @@ - 0.00 0 0 U 0 unclassified -100.00 4 0 - 1 root -100.00 4 0 - 131567 cellular organisms -100.00 4 0 D 2 Bacteria -100.00 4 0 P 1224 Proteobacteria -100.00 4 0 C 1236 Gammaproteobacteria -100.00 4 0 O 91347 Enterobacteriales -100.00 4 0 F 543 Enterobacteriaceae -100.00 4 0 G 561 Escherichia -100.00 4 0 S 562 Escherichia coli -100.00 4 4 - 83333 Escherichia coli K-12 |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/test_database.loc --- a/test-data/test_database.loc Thu Sep 13 09:45:15 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -test_db test_db ${__HERE__} \ No newline at end of file |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/test_db/database.idx |
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| Binary file test-data/test_db/database.idx has changed |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/test_db/database.kdb |
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| Binary file test-data/test_db/database.kdb has changed |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/test_db/taxonomy/names.dmp --- a/test-data/test_db/taxonomy/names.dmp Thu Sep 13 09:45:15 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,74 +0,0 @@ -83333 | Escherichia coli K-12 | | scientific name | -83333 | Escherichia coli K12 | | equivalent name | -562 | "Bacillus coli" Migula 1895 | | authority | -562 | "Bacterium coli commune" Escherich 1885 | | authority | -562 | "Bacterium coli" (Migula 1895) Lehmann and Neumann 1896 | | authority | -562 | ATCC 11775 | | type material | -562 | Bacillus coli | | synonym | -562 | Bacterium coli | | synonym | -562 | Bacterium coli commune | | synonym | -562 | CCUG 24 | | type material | -562 | CCUG 29300 | | type material | -562 | CIP 54.8 | | type material | -562 | DSM 30083 | | type material | -562 | Enterococcus coli | | synonym | -562 | Escherchia coli | | misspelling | -562 | Escherichia coli | | scientific name | -562 | Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | | authority | -562 | Escherichia sp. MAR | | includes | -562 | Escherichia/Shigella coli | | equivalent name | -562 | Eschericia coli | | misspelling | -562 | JCM 1649 | | type material | -562 | LMG 2092 | | type material | -562 | NBRC 102203 | | type material | -562 | NCCB 54008 | | type material | -562 | NCTC 9001 | | type material | -562 | bacterium 10a | | includes | -562 | bacterium E3 | | includes | -561 | Escherchia | | misspelling | -561 | Escherichia | | scientific name | -561 | Escherichia Castellani and Chalmers 1919 | | authority | -543 | Enterobacteraceae | | synonym | -543 | Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev. | | synonym | -543 | Enterobacteriaceae | | scientific name | -543 | Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev. | | synonym | -543 | Enterobacteriaceae Rahn 1937 | | synonym | -543 | gamma-3 proteobacteria | gamma-3 proteobacteria <#1> | in-part | -91347 | 'Enterobacteriales' | | synonym | -91347 | Enterobacteriaceae and related endosymbionts | | synonym | -91347 | Enterobacteriaceae group | | synonym | -91347 | Enterobacteriales | | scientific name | -91347 | enterobacteria | enterobacteria<blast91347> | blast name | -91347 | gamma-3 proteobacteria | gamma-3 proteobacteria <#5> | in-part | -1236 | Gammaproteobacteria | | scientific name | -1236 | Gammaproteobacteria Garrity et al. 2005 | | synonym | -1236 | Proteobacteria gamma subdivision | | synonym | -1236 | Purple bacteria, gamma subdivision | | synonym | -1236 | g-proteobacteria | gamma proteos<blast1236> | blast name | -1236 | gamma proteobacteria | | synonym | -1236 | gamma subdivision | | synonym | -1236 | gamma subgroup | | synonym | -1224 | Proteobacteria | | scientific name | -1224 | Proteobacteria Garrity et al. 2005 | | authority | -1224 | Proteobacteria [class] Stackebrandt et al. 1988 | | authority | -1224 | not Proteobacteria Cavalier-Smith 2002 | | authority | -1224 | proteobacteria | proteobacteria<blast1224> | blast name | -1224 | purple bacteria | | common name | -1224 | purple bacteria and relatives | | common name | -1224 | purple non-sulfur bacteria | | common name | -1224 | purple photosynthetic bacteria | | common name | -1224 | purple photosynthetic bacteria and relatives | | common name | -2 | Bacteria | Bacteria <prokaryote> | scientific name | -2 | Monera | Monera <Bacteria> | in-part | -2 | Procaryotae | Procaryotae <Bacteria> | in-part | -2 | Prokaryota | Prokaryota <Bacteria> | in-part | -2 | Prokaryotae | Prokaryotae <Bacteria> | in-part | -2 | bacteria | bacteria <blast2> | blast name | -2 | eubacteria | | genbank common name | -2 | not Bacteria Haeckel 1894 | | synonym | -2 | prokaryote | prokaryote <Bacteria> | in-part | -2 | prokaryotes | prokaryotes <Bacteria> | in-part | -1 | all | | synonym | -1 | root | | scientific name | -131567 | biota | | synonym | -131567 | cellular organisms | | scientific name | |
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| diff -r 6c09bed3444f -r 1902d3de4a4f test-data/test_db/taxonomy/nodes.dmp --- a/test-data/test_db/taxonomy/nodes.dmp Thu Sep 13 09:45:15 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,10 +0,0 @@ -83333 | 562 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | -562 | 561 | species | EC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | -561 | 543 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | -543 | 91347 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | -91347 | 1236 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | -1236 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | -1224 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | -2 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | -131567 | 1 | no rank | | 8 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | -1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | |
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| diff -r 6c09bed3444f -r 1902d3de4a4f tool-data/kraken_databases.loc.sample --- a/tool-data/kraken_databases.loc.sample Thu Sep 13 09:45:15 2018 -0400 +++ b/tool-data/kraken_databases.loc.sample Wed Dec 04 06:52:03 2019 -0500 |
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| @@ -0,0 +1,18 @@ +# Expect three columns, tab separated, as follows: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (folder name containing the Kraken DB) +# +# e.g. +# plants2018<tab>Plant genomes (2018)<tab>/path/to/krakenDB/plants_2018 +# +# For backward compatibility the Kraken wrapper also accepts: +# - value (Galaxy records this in the Galaxy DB) +# - name (Final part of folder name, Galaxy shows this in the UI) +# - path (Parent folder name, where $path/$name contains the Kraken DB) +# +# e.g. +# plants2018<tab>plants_2018<tab>/path/to/krakenDB +# +# Please avoid this legacy usage, as not all tools using +# the kraken_databases.loc file will understand it. |