Mercurial > repos > iuc > kraken2
changeset 4:e674066930b2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 055a83d01b077101110272c44ef0ff2a04d5d1d4"
| author | iuc |
|---|---|
| date | Wed, 17 Feb 2021 17:39:37 +0000 |
| parents | 4a9da2b6c2e3 |
| children | 20e2f64aa1fe |
| files | kraken2.xml test-data/kraken_test2_report.tab |
| diffstat | 2 files changed, 21 insertions(+), 9 deletions(-) [+] |
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--- a/kraken2.xml Mon Nov 23 20:50:12 2020 +0000 +++ b/kraken2.xml Wed Feb 17 17:39:37 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy0"> +<tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy1"> <description> assign taxonomic labels to sequencing reads </description> @@ -68,8 +68,8 @@ #if $report.create_report: --report '${report_output}' $report.use_mpa_style - $report.report_zero_counts: - $report.report_minimizer_data: + $report.report_zero_counts + $report.report_minimizer_data #end if > '${output}' @@ -132,16 +132,16 @@ <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> </data> - <data name="out1.1" format_source="input_pair['forward']" label="Unclassified forward" from_work_dir="un_out_1.*"> + <data name="out1_1" format_source="input_pair['forward']" label="Unclassified forward" from_work_dir="un_out_1.*"> <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> </data> - <data name="out2.1" format_source="input_pair['forward']" label="Unclassified reverse" from_work_dir="un_out_2.*"> + <data name="out2_1" format_source="input_pair['forward']" label="Unclassified reverse" 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="Classified forward" from_work_dir="cl_out_1.*"> + <data name="out3_1" format_source="input_pair['forward']" label="Classified forward" from_work_dir="cl_out_1.*"> <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> </data> - <data name="out4.1" format_source="input_pair['forward']" label="Classified reverse" from_work_dir="cl_out_2.*"> + <data name="out4_1" format_source="input_pair['forward']" label="Classified reverse" from_work_dir="cl_out_2.*"> <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> </data> @@ -155,7 +155,6 @@ <param name="split_reads" value="false"/> <param name="quick" value="no"/> <param name="confidence" value=".2"/> - <param name="only-classified-output" value="false"/> <param name="kraken2_database" value="test_entry"/> <output name="output" file="kraken_test1_output.tab" ftype="tabular"/> </test> @@ -166,13 +165,25 @@ <param name="split_reads" value="true"/> <param name="quick" value="no"/> <param name="confidence" value="0"/> - <param name="only-classified-output" value="false"/> <param name="kraken2_database" value="test_entry"/> <output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/> <output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/> <output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/> <output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/> <output name="output" file="kraken_test2_output.tab" ftype="tabular"/> + + </test> + <test> + <param name="single_paired_selector" value="yes"/> + <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/> + <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/> + <param name="use-names" value="true"/> + <section name="report"> + <param name="create_report" value="true"/> + <param name="report_minimizer_data" value="true"/> + </section> + <param name="kraken2_database" value="test_entry"/> + <output name="report_output" file="kraken_test2_report.tab" ftype="tabular"/> </test> </tests> <help>