| Previous changeset 0:3fe0d1df3950 (2022-08-24) Next changeset 2:b1ca81ce88f9 (2022-10-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit 8417888e4ecc1fd033d3412957c5475e29f66403 |
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modified:
vapor.xml |
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added:
test-data/test_reads.fastqsanger.gz |
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| diff -r 3fe0d1df3950 -r 7bf891a13ace test-data/test_reads.fastqsanger.gz |
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| Binary file test-data/test_reads.fastqsanger.gz has changed |
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| diff -r 3fe0d1df3950 -r 7bf891a13ace vapor.xml --- a/vapor.xml Wed Aug 24 09:51:46 2022 +0000 +++ b/vapor.xml Sat Oct 01 14:11:42 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy0" profile="21.05"> +<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy1" profile="21.05"> <description> Classify Influenza samples from raw short read sequence data </description> @@ -29,7 +29,7 @@ ]]> </command> <inputs> <param name="fasta_file" format="fasta" type="data" label="FASTA file" help="Raw short read sequences (full length reference segment sequences)" /> - <param name="fastq_file" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file(s)" help="WGS reads" /> + <param name="fastq_file" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" multiple="true" label="FASTQ file(s)" help="WGS reads" /> <param name="output_type" type="select" label="Output type"> <option value="scores" selected="true">Return scores only</option> <option value="fasta">Return FASTA only</option> @@ -44,13 +44,13 @@ </section> </inputs> <outputs> - <data name="output_scores" from_work_dir="out_file" format="tabular" label="VAPOR: closest reference"> + <data name="output_scores" from_work_dir="out_file" format="tabular" label="${tool.name} on ${on_string}: closest reference scores"> <filter>output_type == "scores"</filter> <actions> <action name="column_names" type="metadata" default="% of query bases in reads,Total score,Query length,Mean score,Reads after culling,Query description" /> </actions> </data> - <data name="output_fasta" from_work_dir="out_file" format="fasta" label="VAPOR: closest reference (fasta)"> + <data name="output_fasta" from_work_dir="out_file" format="fasta" label="${tool.name} on ${on_string}: closest reference fasta"> <filter>output_type == "fasta"</filter> </data> </outputs> @@ -62,6 +62,11 @@ </test> <test expect_num_outputs="1"> <param name="fasta_file" value="HA_sample.fa" /> + <param name="fastq_file" value="test_reads.fastqsanger.gz" /> + <output name="output_scores" file="output1.tab" /> + </test> + <test expect_num_outputs="1"> + <param name="fasta_file" value="HA_sample.fa" /> <param name="fastq_file" value="test_reads.fq" /> <section name="opt"> <param name="kmer_length" value="29" /> |