| Previous changeset 5:20e2f64aa1fe (2024-02-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 3c6cc780d2d8ea156d167289cc2576fc3e43d2fd |
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modified:
kraken2.xml macros.xml |
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| diff -r 20e2f64aa1fe -r cdee7158adf3 kraken2.xml --- a/kraken2.xml Fri Feb 09 21:43:22 2024 +0000 +++ b/kraken2.xml Thu Jun 06 09:03:24 2024 +0000 |
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| @@ -135,18 +135,16 @@ <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> </data> - <data name="out1_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified forward read collection" from_work_dir="un_out_1.*"> + <collection name="out_unclassified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Unclassified read pairs"> + <data name="forward" from_work_dir="un_out_1.*"/> + <data name="reverse" from_work_dir="un_out_2.*"/> <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> - </data> - <data name="out2_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified reverse read collection" from_work_dir="un_out_2.*"> - <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> - </data> - <data name="out3_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified forward read collection" from_work_dir="cl_out_1.*"> + </collection> + <collection name="out_classified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Classified read pairs"> + <data name="forward" from_work_dir="cl_out_1.*"/> + <data name="reverse" from_work_dir="cl_out_2.*"/> <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> - </data> - <data name="out4_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified reverse read collection" from_work_dir="cl_out_2.*"> - <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> - </data> + </collection> <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/> <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> @@ -175,6 +173,29 @@ <output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/> <output name="output" file="kraken_test2_output.tab" ftype="tabular"/> </test> + <!-- same test but collection in/output --> + <test expect_num_outputs="7"> + <param name="single_paired_selector" value="collection"/> + <param name="input_pair"> + <collection type="paired"> + <element name="forward" value="kraken_test2_R1.fastq" ftype="fastq"/> + <element name="reverse" value="kraken_test2_R2.fastq" ftype="fastq"/> + </collection> + </param> + <param name="split_reads" value="true"/> + <param name="quick" value="no"/> + <param name="confidence" value="0"/> + <param name="kraken2_database" value="test_entry"/> + <output_collection name="out_unclassified_paired" type="paired"> + <element name="forward" file="un_test2_output_1.fastq" ftype="fastq"/> + <element name="reverse" file="un_test2_output_2.fastq" ftype="fastq"/> + </output_collection> + <output_collection name="out_classified_paired" type="paired"> + <element name="forward" file="cl_test2_output_1.fastq" ftype="fastq"/> + <element name="reverse" file="cl_test2_output_2.fastq" ftype="fastq"/> + </output_collection> + <output name="output" file="kraken_test2_output.tab" ftype="tabular"/> + </test> <test expect_num_outputs="2"> <param name="single_paired_selector" value="yes"/> <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/> |
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| diff -r 20e2f64aa1fe -r cdee7158adf3 macros.xml --- a/macros.xml Fri Feb 09 21:43:22 2024 +0000 +++ b/macros.xml Thu Jun 06 09:03:24 2024 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">2.1.1</token> + <token name="@TOOL_VERSION@">2.1.3</token> <token name="@INTYPES@">fasta,fastq,fasta.gz,fasta.bz2,fastq.gz,fastq.bz2</token> <xml name="input_database"> <param label="Select a Kraken2 database" name="kraken2_database" type="select"> |