| Previous changeset 7:241a78eb2935 (2025-05-26) Next changeset 9:cbe396d9773e (2025-12-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 658f57a9c3a3698d4e6cfa15eeeb3ec8647e054e |
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modified:
kraken2.xml macros.xml |
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added:
test-data/kraken_test1_cl.fas test-data/kraken_test1_un.fas test-data/kraken_test2_R1.fastq.gz test-data/kraken_test2_R2.fastq.gz |
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| diff -r 241a78eb2935 -r e150ae930235 kraken2.xml --- a/kraken2.xml Mon May 26 08:00:46 2025 +0000 +++ b/kraken2.xml Tue Aug 19 19:58:36 2025 +0000 |
| [ |
| b'@@ -1,5 +1,4 @@\n-<?xml version="1.0"?>\n-<tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy1">\n+<tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>\n assign taxonomic labels to sequencing reads\n </description>\n@@ -15,35 +14,13 @@\n <version_command>kraken2 --version</version_command>\n <command detect_errors="exit_code">\n <![CDATA[\n-\n- #def get_type($data)\n- #if $data.is_of_type(\'fastq\'):\n- #return \'fastq\'\n- #elif $data.is_of_type(\'fasta\'):\n- #return \'fasta\'\n- #elif $data.is_of_type(\'fastqsanger\'):\n- #return \'fastqsanger\'\n- #elif $data.is_of_type(\'fasta.gz\'):\n- #return \'fasta.gz\'\n- #elif $data.is_of_type(\'fasta.bz2\'):\n- #return \'fasta.bz2\'\n- #elif $data.is_of_type(\'fastq.gz\'):\n- #return \'fastq.gz\'\n- #elif $data.is_of_type(\'fastq.bz2\'):\n- #return \'fastq.bz2\'\n- #end if\n- #end def\n-\n kraken2\n --threads \\${GALAXY_SLOTS:-1}\n --db \'${kraken2_database.fields.path}\'\n \n $quick\n \n- #if $single_paired.single_paired_selector == "yes"\n- --paired \n- \'${single_paired.forward_input}\' \'${single_paired.reverse_input}\'\n- #elif $single_paired.single_paired_selector == "collection":\n+ #if $single_paired.single_paired_selector == "collection":\n --paired \n \'${single_paired.input_pair.forward}\' \'${single_paired.input_pair.reverse}\'\n #else:\n@@ -52,13 +29,11 @@\n \n #if $split_reads:\n #if $single_paired.single_paired_selector == "no":\n- --classified-out \'${classified_out_s}\' --unclassified-out \'${unclassified_out_s}\'\n- #elif $single_paired.single_paired_selector == "yes":\n- #set $result = $get_type($single_paired.forward_input)\n- --unclassified-out \'un_out#.${result}\' --classified-out \'cl_out#.${result}\'\n+ --unclassified-out \'un_out\'\n+ --classified-out \'cl_out\'\n #else:\n- #set $result = $get_type($single_paired.input_pair.forward)\n- --unclassified-out \'un_out#.${result}\' --classified-out \'cl_out#.${result}\'\n+ --unclassified-out \'un_out#\'\n+ --classified-out \'cl_out#\'\n #end if\n #end if\n \n@@ -76,21 +51,42 @@\n #end if\n \n > \'${output}\'\n+\n+ #if $split_reads:\n+ #if $single_paired.single_paired_selector == "no":\n+ #if $single_paired.input_sequences.ext.endswith(".gz")\n+ #set command = "gzip -c"\n+ #elif $single_paired.input_sequences.ext.endswith(".bz2")\n+ #set command = "bzip2 -c"\n+ #else\n+ #set command = "cat"\n+ #end if\n+ && $command un_out > \'$unclassified_out_s\'\n+ && $command cl_out > \'$classified_out_s\'\n+ #else:\n+ #if $single_paired.input_pair.forward.ext.endswith(".gz")\n+ #set command = "gzip -c"\n+ #elif $single_paired.input_pair.forward.ext.endswith(".bz2")\n+ #set command = "bzip2 -c"\n+ #else\n+ #set command = "cat"\n+ #end if\n+ && $command un_out_1 > \'$out_unclassified_paired.forward\'\n+ && $command un_out_2 > \'$out_unclassified_paired.reverse\'\n+ && $command cl_out_1 > \'$out_classified_paired.forward\'\n+ && $command cl_out_1 > \'$out_classified_paired.forward\'\n+ #end if\n+ #end if\n ]]></command>\n <inputs>\n <conditional name="single_paired">\n '..b'out4" file="cl_test2_output_2.fastq" ftype="fastq"/>\n- <output name="output" file="kraken_test2_output.tab" ftype="tabular"/>\n+ <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>\n+ <output name="classified_out_s" file="kraken_test1_cl.fas" ftype="fasta"/>\n+ <output name="unclassified_out_s" file="kraken_test1_un.fas" ftype="fasta"/>\n </test>\n- <!-- same test but collection in/output -->\n+\n <test expect_num_outputs="7">\n- <param name="single_paired_selector" value="collection"/>\n- <param name="input_pair">\n- <collection type="paired">\n- <element name="forward" value="kraken_test2_R1.fastq" ftype="fastq"/>\n- <element name="reverse" value="kraken_test2_R2.fastq" ftype="fastq"/>\n- </collection>\n- </param>\n+ <conditional name="single_paired">\n+ <param name="single_paired_selector" value="collection"/>\n+ <param name="input_pair">\n+ <collection type="paired">\n+ <element name="forward" value="kraken_test2_R1.fastq.gz" ftype="fastqsanger.gz"/>\n+ <element name="reverse" value="kraken_test2_R2.fastq.gz" ftype="fastqsanger.gz"/>\n+ </collection>\n+ </param>\n+ <param name="single_paired_selector" value="collection"/>\n+ </conditional>\n <param name="split_reads" value="true"/>\n <param name="quick" value="no"/>\n <param name="confidence" value="0"/>\n <param name="kraken2_database" value="test_entry"/>\n <output_collection name="out_unclassified_paired" type="paired">\n- <element name="forward" file="un_test2_output_1.fastq" ftype="fastq"/>\n- <element name="reverse" file="un_test2_output_2.fastq" ftype="fastq"/>\n+ <element name="forward" file="un_test2_output_1.fastq" ftype="fastqsanger.gz" decompress="true"/>\n+ <element name="reverse" file="un_test2_output_2.fastq" ftype="fastqsanger.gz" decompress="true"/>\n </output_collection>\n <output_collection name="out_classified_paired" type="paired">\n- <element name="forward" file="cl_test2_output_1.fastq" ftype="fastq"/>\n- <element name="reverse" file="cl_test2_output_2.fastq" ftype="fastq"/>\n+ <element name="forward" file="cl_test2_output_1.fastq" ftype="fastqsanger.gz" decompress="true"/>\n+ <element name="reverse" file="cl_test2_output_2.fastq" ftype="fastqsanger.gz" decompress="true"/>\n </output_collection>\n <output name="output" file="kraken_test2_output.tab" ftype="tabular"/>\n+ <assert_command>\n+ <has_text text="gzip -c"/>\n+ </assert_command>\n </test>\n+\n <test expect_num_outputs="2">\n- <param name="single_paired_selector" value="yes"/>\n- <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/>\n- <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/>\n- <param name="use-names" value="true"/>\n+ <conditional name="single_paired">\n+ <param name="single_paired_selector" value="collection"/>\n+ <param name="input_pair">\n+ <collection type="paired">\n+ <element name="forward" value="kraken_test2_R1.fastq" ftype="fastqsanger"/>\n+ <element name="reverse" value="kraken_test2_R2.fastq" ftype="fastqsanger"/>\n+ </collection>\n+ </param>\n+ </conditional>\n+ <param name="use_names" value="true"/>\n <section name="report">\n <param name="create_report" value="true"/>\n <param name="report_minimizer_data" value="true"/>\n' |
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| diff -r 241a78eb2935 -r e150ae930235 macros.xml --- a/macros.xml Mon May 26 08:00:46 2025 +0000 +++ b/macros.xml Tue Aug 19 19:58:36 2025 +0000 |
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| @@ -1,7 +1,9 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">2.1.3</token> - <token name="@INTYPES@">fasta,fastq,fasta.gz,fasta.bz2,fastq.gz,fastq.bz2</token> + <token name="@VERSION_SUFFIX@">2</token> + <token name="@PROFILE@">24.0</token> + <token name="@INTYPES@">fasta,fasta.gz,fasta.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2</token> <xml name="input_database"> <param label="Select a Kraken2 database" name="kraken2_database" type="select"> <options from_data_table="kraken2_databases"> |
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| diff -r 241a78eb2935 -r e150ae930235 test-data/kraken_test1_un.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken_test1_un.fas Tue Aug 19 19:58:36 2025 +0000 |
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| @@ -0,0 +1,8 @@ +>gi|145231|gb|M33724.1|ECOALPHOA Escherichia coli K-12 truncated PhoA (phoA) gene, partial cds; and transposon Mu dI, partial sequence +CAAAGCTCCGGGCCTCACCCAGGCGCTAAATACCAAAGATGGCGCAGTGATGGTGATGAGTTACGGGAACTCCGAAGAGGATTCACAAGAACATACCGGCAGTCAGTTGCGTATTGCGGCGTATGGCCCGCATGCCGCCAATGAAGCGGCGCACGAAAAACGCGAAAGCGT +>gi|145232|gb|M33725.1|ECOALPHOB Escherichia coli K12 phoA pseudogene and transposon Mu dl-R, partial sequence +CTGTCATAAAGTTGTCACGGCCGAGACTTATAGTCGCTTTGTTTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAAACAAAGCACTATTGCACTGGCACTCTTACCGTTACTGTTTACCCCTGTGACAAAAGCCCGGACACCAGTGAAGCGGCGCACGAAAAACGCGAAAGCGT +>gi|145234|gb|M33727.1|ECOALPHOE Escherichia coli K12 upstream sequence of psiA5::Mu dI. is identical to psiA30 upstream sequence; putative (phoA) pseudogene and transposon Mu dl-R, partial sequence +TTGTTTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAAACAAAGCACTATTGCACTGGTGAAGCGGCGCACGAAAAACGCGAAAGCGT +>gi|146195|gb|J01619.1|ECOGLTA Eschericia coli gltA gene, sdhCDAB operon and sucABCD operons, complete sequence +GAATTCGACCGCCATTGCGCAAGGCATCGCCATGACCAGGCAGGATACAAAAGAGAGTCGATAAATATTCACGGTGTCCATACCTGATAAATATTTTATGAAAGGCGGCGATGATGCCGCAAAATAATACTTATTTATAATCCAGCACGTAGGTTGCGTTAGCGGTTACTTCACCTGCCGTGACATCGACTGCATTATCAATTTGTTCCATCCAGGCGAAAAAGTTCAGCGTCTGTTCTGATGAGCTTGCATCCAGGTCAAGATCTGGCGCGGCTGAACCTAATACGATGTTACCGTCATTTTTGTCCATCAGTCGTACACCGACCCCAGTTGCTTCGCCTGCACTGGTGTTGCTCAACAAAGGCGTAGCACCAGTTGTCTTAGCCGTGCTATCGAAGGTTACGCCAAACTTTGGATACCGGCATTCCGCTACCGTTGTCAGAAGCAGGCAGATCACAGTTGATCAAGCGAATGTCGACGGCCACTTTATTGCTATGATGCTCCCGGTTTATATGGGTTGTCGTGACTTGTCCAAGATCTATGTTTTTATCAATATCTTCTGGATGAATTTCACAAGGTGCTTCAATAACCTCCCCCTTAAAGTGAATTTCGCCAGAACCTTCATCAGCAGCATAAACAGGTGCAGTGAACAGCAGAGATACGGCCAGTGCGGCCAATGTTTTTTGTCCTTTAAACATAACAGAGTCCTTTAAGGATATAGAATAGGGGTATAGCTACGCCAGAATATCGTATTTGATTATTGCTAGTTTTTAGTTTTGCTTAAAAAATATTGTTAGTTTTATTAAATTGGAAAACTAAATTATTGGTATCATGAATTGTTGTATGATGATAAATATAGGGGGGATATGATAGACGTCATTTTCATAGGGTTATAAAATGCGACTACCATGAAGTTTTTAATTCAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAAGTTTTTTGTGTTTAGGCATATAAAAATCAAGCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAGCAATCGAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAGTGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCGCTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTTCAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAGGTCATCCTTCGTGCCCAGCTCTTTCAGCACTTCATGGCAGGTTTCACGCATTACGGTGGCGCGCGGGTCGTAATTTTTGTACACGCGGTGACCGAAGCCCATCAGGCGGAAAGAATCATTTTTGTCTTTCGCACGACGAAAAAATTCCGGAATGTGTTTAACGGAGCTGATTTCTTCCAGCATTTTCAGCGCCGCTTCGTTAGCACCGCCGTGCGCAGGTCCCCACAGTGAAGCAATACCTGCTGCGATACAGGCAAACGGGTTCGCACCCGAAGAGCCAGCGGTACGCACGGTGGAGGTAGAGGCGTTCTGTTCATGGTCAGCGTGCAGGATCAGAATACGGTCCATAGCACGTTCCAGAATCGGATTAACTTCATACGGTTCGCACGGCGTGGAGAACATCATATTCAGGAAGTTACCGGCGTAGGAGAGATCGTTGCGCGGGTAAACAAATGGCTGACCAATGGAATACTTGTAACACATCGCGGCCATGGTCGGCATTTTCGACAGCAGGCGGAACGCGGCAATTTCACGGTGACGAGGATTGTTAACATCCAGCGAGTCGTGATAGAACGCCGCCAGCGCGCCGGTAATACCACACATGACTGCCATTGGATGCGAGTCGCGACGGAAAGCATGGAACAGACGGGTAATCTGCTCGTGGATCATGGTATGACGGGTCACCGTAGTTTTAAATTCGTCATACTGTTCCTGAGTCGGTTTTTCACCATTCAGCAGGATGTAACAAACTTCCAGGTAGTTAGAATCGGTCGCCAGCTGATCGATCGGGAAACCGCGGTGCAGCAAAATACCTTCATCACCATCAATAAAAGTAATTTTAGATTCGCAGGATGCGGTTGAAGTGAAGCCTGGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTCGCCGCTCTGTGAAAGAGGGGAAAACCTGGGTACAGAGCTCTGGGCGCTTGCAGGTAAAGGATCCATTGATGACGAATAAATGGCGAATCAAGTACTTAGCAATCCGAATTATTAAACTTGTCTACCACTAATAACTGTCCCGAATGAATTGGTCAATACTCCACACTGTTACATAAGTTAATCTTAGGTGAAATACCGACTTCATAACTTTTACGCATTATATGCTTTTCCTGGTAATGTTTGTAACAACTTTGTTGAATGATTGTCAAATTAGATGATTAAAAATTAAATAAATGTTGTTATCGTGACCTGGATCACTGTTCAGGATAAAACCCGACAAACTATATGTAGGTTAATTGTAATGATTTTGTGAACAGCCTATACTGCCGCCAGTCTCCGGAACACCCTGCAATCCCGAGCCACCCAGCGTTGTAACGTGTCGTTTTCGCATCTGGAAGCAGTGTTTTGCATGACGCGCAGTTATAGAAAGGACGCTGTCTGACCCGCAAGCAGACCGGAGGAAGGAAATCCCGACGTCTCCAGGTAACAGAAAGTTAACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAGAACAGCATGTGGGCGTTATTCATGATAAGAAATGTGAAAAAACAAAGACCTGTTAATCTGGACCTACAGACCATCCGGTTCCCCATCACGGCGATAGCGTCCATTCTCCATCGCGTTTCCGGTGTGATCACCTTTGTTGCAGTGGGCATCCTGCTGTGGCTTCTGGGTACCAGCCTCTCTTCCCCTGAAGGTTTCGAGCAAGCTTCCGCGATTATGGGCAGCTTCTTCGTCAAATTTATCATGTGGGGCATCCTTACCGCTCTGGCGTATCACGTCGTCGTAGGTATTCGCCACATGATGATGGATTTTGGCTATCTGGAAGAAACATTCGAAGCGGGTAAACGCTCCGCCAAAATCTCCTTTGTTATTACTGTCGTGCTTTCACTTCTCGCAGGAGTCCTCGTATGGTAAGCAACGCCTCCGCATTAGGACGCAATGGCGTACATGATTTCATCCTCGTTCGCGCTACCGCTATCGTCCTGACGCTCTACATCATTTATATGGTCGGTTTTTTCGCTACCAGTGGCGAGCTGACATATGAAGTCTGGATCGGTTTCTTCGCCTCTGCGTTCACCAAAGTGTTCACCCTGCTGGCGCTGTTTTCTATCTTGATCCATGCCTGGATCGGCATGTGGCAGGTGTTGACCGACTACGTTAAACCGCTGGCTTTGCGCCTGATGCTGCAACTGGTGATTGTCGTTGCACTGGTGGTTTACGTGATTTATGGATTCGTTGTGGTGTGGGGTGTGTGATGAAATTGCCAGTCAGAGAATTTGATGCAGTTGTGATTG |
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| diff -r 241a78eb2935 -r e150ae930235 test-data/kraken_test2_R1.fastq.gz |
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| diff -r 241a78eb2935 -r e150ae930235 test-data/kraken_test2_R2.fastq.gz |
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