| Previous changeset 4:e674066930b2 (2021-02-17) Next changeset 6:cdee7158adf3 (2024-06-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit b5beeef6c90fe39ce3ace531877d632725839ee4 |
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modified:
kraken2.xml |
| b |
| diff -r e674066930b2 -r 20e2f64aa1fe kraken2.xml --- a/kraken2.xml Wed Feb 17 17:39:37 2021 +0000 +++ b/kraken2.xml Fri Feb 09 21:43:22 2024 +0000 |
| [ |
| @@ -6,6 +6,9 @@ <macros> <import>macros.xml</import> </macros> + <xrefs> + <xref type="bio.tools">kraken2</xref> + </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> </requirements> @@ -115,33 +118,33 @@ <data name="unclassified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads"> <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter> </data> - <data name="report_output" format="tabular" label="Report: ${tool.name} on ${on_string}"> + <data name="report_output" format="tabular" label="${tool.name} on ${on_string}: Report"> <filter>(report['create_report'])</filter> </data> - <data name="out1" format_source="forward_input" label="Unclassified forward" from_work_dir="un_out_1.*"> + <data name="out1" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified forward reads" from_work_dir="un_out_1.*"> <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> </data> - <data name="out2" format_source="forward_input" label="Unclassified reverse" from_work_dir="un_out_2.*"> + <data name="out2" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified reverse reads" from_work_dir="un_out_2.*"> <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> </data> - <data name="out3" format_source="forward_input" label="Classified forward" from_work_dir="cl_out_1.*"> + <data name="out3" format_source="forward_input" label="${tool.name} on ${on_string}: Classified forward reads" from_work_dir="cl_out_1.*"> <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> </data> - <data name="out4" format_source="forward_input" label="Classified reverse" from_work_dir="cl_out_2.*"> + <data name="out4" format_source="forward_input" label="${tool.name} on ${on_string}: Classified reverse reads" from_work_dir="cl_out_2.*"> <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> </data> - <data name="out1_1" format_source="input_pair['forward']" label="Unclassified forward" from_work_dir="un_out_1.*"> + <data name="out1_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified forward read collection" from_work_dir="un_out_1.*"> <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> </data> - <data name="out2_1" format_source="input_pair['forward']" label="Unclassified reverse" from_work_dir="un_out_2.*"> + <data name="out2_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified reverse read collection" from_work_dir="un_out_2.*"> <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> </data> - <data name="out3_1" format_source="input_pair['forward']" label="Classified forward" from_work_dir="cl_out_1.*"> + <data name="out3_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified forward read collection" from_work_dir="cl_out_1.*"> <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> </data> - <data name="out4_1" format_source="input_pair['forward']" label="Classified reverse" from_work_dir="cl_out_2.*"> + <data name="out4_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified reverse read collection" from_work_dir="cl_out_2.*"> <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> </data> @@ -149,7 +152,7 @@ <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="single_paired_selector" value="no"/> <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/> <param name="split_reads" value="false"/> @@ -158,7 +161,7 @@ <param name="kraken2_database" value="test_entry"/> <output name="output" file="kraken_test1_output.tab" ftype="tabular"/> </test> - <test> + <test expect_num_outputs="5"> <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"/> @@ -171,9 +174,8 @@ <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> + <test expect_num_outputs="2"> <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"/> |