| Previous changeset 6:31fa26c0692b (2021-06-08) Next changeset 8:5ae3496f9ca3 (2021-08-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" |
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modified:
macros.xml meryl.xml |
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added:
test-data/child.fasta.gz |
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| diff -r 31fa26c0692b -r 51c2360aa807 macros.xml --- a/macros.xml Tue Jun 08 07:20:29 2021 +0000 +++ b/macros.xml Mon Jun 28 09:32:16 2021 +0000 |
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| @@ -1,6 +1,7 @@ <macros> <token name="@TOOL_VERSION@">1.3</token> - <token name="@GALAXY_TOOL_VERSION@">galaxy2</token> + <token name="@GALAXY_TOOL_VERSION@">galaxy</token> + <token name="@SUFFIX_VERSION@">3</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0196</edam_topic> |
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| diff -r 31fa26c0692b -r 51c2360aa807 meryl.xml --- a/meryl.xml Tue Jun 08 07:20:29 2021 +0000 +++ b/meryl.xml Mon Jun 28 09:32:16 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'> +<tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@' profile='20.01'> <description>a genomic k-mer counter and sequence utility</description> <macros> <import>macros.xml</import> @@ -153,7 +153,7 @@ <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option> <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option> </param> - <param name="input_reads" type="data" format="fastq,fasta" label="Input sequences" help="Select your reads in FASTA/FASTQ format." /> + <param name="input_reads" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Input sequences" help="Select your reads in FASTA/FASTQ format." /> <conditional name="options_kmer_size"> <param name="kmer_size" type="select" label="K-mer size selector"> <option value="provide">Set a k-mer size</option> @@ -225,9 +225,9 @@ <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" /> </when> <when value="trio-mode"> - <param name="child_reads" type="data" format="fastq,fasta" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly" /> - <param name="paternal_reads" type="data" format="fastq,fasta" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly" /> - <param name="maternal_reads" type="data" format="fastq,fasta" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly" /> + <param name="child_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly" /> + <param name="paternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly" /> + <param name="maternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly" /> <conditional name="options_kmer_size"> <param name="kmer_size" type="select" label="K-mer size selector"> <option value="provide">Set a k-mer size</option> @@ -427,7 +427,7 @@ </assert_contents> </output> </test> - <!-- test 11 --> + <!-- test 12 --> <test expect_num_outputs="1"> <conditional name="operation_type"> <param name="command_type" value="arithmetic-kmers" /> @@ -437,7 +437,7 @@ </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> - <has_size value="37172" delta="300" /> + <has_size value="37501" delta="300" /> </assert_contents> </output> </test> @@ -619,6 +619,26 @@ </conditional> <output name="read_db_print" file="output_25.read-db.tabular" sort="True"/> </test> + <!--Test compressed files--> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="count-kmers" /> + <param name="count_operation" value="count" /> + <param name="input_reads" value="child.fasta.gz" /> + <conditional name="options_kmer_size"> + <param name="kmer_size" value="provide" /> + <param name="input_kmer_size" value="7" /> + </conditional> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="1851" delta="300" /> + </assert_contents> + </output> + <assert_stdout> + <has_line line="K-mer size: 7" /> + </assert_stdout> + </test> </tests> <help><![CDATA[ |
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| diff -r 31fa26c0692b -r 51c2360aa807 test-data/child.fasta.gz |
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| Binary file test-data/child.fasta.gz has changed |