Mercurial > repos > iuc > kma
changeset 3:0e8330535ea0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 8c23e6a057edc7697f51ccabba16fb4fdabbab71
| author | iuc |
|---|---|
| date | Wed, 23 Jul 2025 12:20:33 +0000 |
| parents | 98099e4da1fd |
| children | |
| files | kma_map.xml macros.xml test-data/ERR884056_ecoli_b0842.mapped_R1.fastq.gz |
| diffstat | 3 files changed, 68 insertions(+), 24 deletions(-) [+] |
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--- a/kma_map.xml Fri Jun 14 21:15:44 2024 +0000 +++ b/kma_map.xml Wed Jul 23 12:20:33 2025 +0000 @@ -10,11 +10,9 @@ <command detect_errors="exit_code"> <![CDATA[ kma - -t \${GALAXY_SLOTS:-1} + -t "\${GALAXY_SLOTS:-1}" -t_db '${kma_index.fields.path}' - #if $single_paired.single_paired_selector == 'paired' - -ipe '${single_paired.forward_input}' '${single_paired.reverse_input}' - #elif $single_paired.single_paired_selector == "paired_collection": + #if $single_paired.single_paired_selector == "paired_collection": -ipe '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}' #else: -i '${single_paired.input_sequences}' @@ -76,15 +74,10 @@ <conditional name="single_paired"> <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired"> <option value="paired_collection">Paired collection</option> - <option value="paired">Paired-end data</option> <option selected="True" value="single">Single-end data</option> </param> <when value="paired_collection"> - <param argument="-ipe" format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" /> - </when> - <when value="paired"> - <param argument="-ipe" format="@INTYPES@" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/> - <param argument="-ipe" format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/> + <param argument="-ipe" format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Paired reads" help="FASTQ datasets" /> </when> <when value="single"> <param argument="-i" format="@INTYPES@" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/> @@ -138,10 +131,14 @@ </outputs> <tests> <test expect_num_outputs="4"> - <param name="single_paired_selector" value="single"/> - <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/> - <param name="advanced" value="advanced"/> - <param name="kmer_size" value="8"/> + <conditional name="single_paired"> + <param name="single_paired_selector" value="single"/> + <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/> + </conditional> + <conditional name="settings"> + <param name="advanced" value="advanced"/> + <param name="kmer_size" value="8"/> + </conditional> <param name="kma_index" value="test_index"/> <output name="result_overview" ftype="tabular"> <assert_contents> @@ -174,15 +171,19 @@ </output> </test> <test expect_num_outputs="5"> - <param name="single_paired_selector" value="single"/> - <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/> - <param name="advanced" value="advanced"/> - <param name="kmer_size" value="8"/> - <param name="matrix" value="true"/> + <conditional name="single_paired"> + <param name="single_paired_selector" value="single"/> + <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/> + </conditional> + <conditional name="settings"> + <param name="advanced" value="advanced"/> + <param name="kmer_size" value="8"/> + <param name="matrix" value="true"/> + </conditional> <param name="kma_index" value="test_index"/> <output name="assembly_matrix" ftype="tabular"> <assert_contents> - <has_n_lines n="2553"/> + <has_n_lines n="2551"/> <has_n_columns n="7" comment="#"/> <has_line_matching expression="^A	.*"/> <has_line_matching expression="^T	.*"/> @@ -191,6 +192,51 @@ </assert_contents> </output> </test> + <test expect_num_outputs="4"> + <conditional name="single_paired"> + <param name="single_paired_selector" value="paired_collection"/> + <param name="input_pair"> + <collection type="paired"> + <element name="forward" value="ERR884056_ecoli_b0842.mapped_R1.fastq.gz"/> + <element name="reverse" value="ERR884056_ecoli_b0842.mapped_R1.fastq.gz"/> + </collection> + </param> + </conditional> + <conditional name="settings"> + <param name="advanced" value="advanced"/> + <param name="kmer_size" value="8"/> + </conditional> + <param name="kma_index" value="test_index"/> + <output name="result_overview" ftype="tabular"> + <assert_contents> + <has_n_lines n="4"/> + <has_n_columns n="11"/> + <has_text text="#Template"/> + <has_text text="b0842_1"/> + </assert_contents> + </output> + <output name="consensus_alignment" ftype="txt"> + <assert_contents> + <has_n_lines n="255"/> + <has_text text="b0842_1"/> + <has_text text="query" n="63"/> + <has_text text="template" n="63"/> + </assert_contents> + </output> + <output name="consensus_sequences" ftype="fasta"> + <assert_contents> + <has_line_matching expression="^>.*" n="3"/> + <has_line_matching expression="^>b0842_1"/> + </assert_contents> + </output> + <output name="read_mapping" ftype="tabular"> + <assert_contents> + <has_n_lines n="1012"/> + <has_n_columns n="7"/> + <has_text text="b0842_1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[
--- a/macros.xml Fri Jun 14 21:15:44 2024 +0000 +++ b/macros.xml Wed Jul 23 12:20:33 2025 +0000 @@ -1,8 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">1.4.14</token> - <token name="@INTYPES@"> - fastq,fastq.gz,fastqsanger,fastqsanger.gz - </token> + <token name="@TOOL_VERSION@">1.5.1</token> + <token name="@INTYPES@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token> <xml name="kma_index"> <param label="Select a KMA index" name="kma_index" type="select"> <options from_data_table="kma_index">