Mercurial > repos > iuc > kma
changeset 2:3cd89604dffd draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma commit f040316174672d9e3ce53b1873ab07cff1128940
| author | iuc |
|---|---|
| date | Mon, 15 Dec 2025 21:59:27 +0000 |
| parents | 4b3fca68379b |
| children | |
| files | kma_map.xml macros.xml test-data/ERR884056_ecoli_b0842.mapped_R1.fastq.gz |
| diffstat | 3 files changed, 136 insertions(+), 58 deletions(-) [+] |
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--- a/kma_map.xml Sat Nov 27 09:35:27 2021 +0000 +++ b/kma_map.xml Mon Dec 15 21:59:27 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy1"> +<tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description></description> <macros> <import>macros.xml</import> @@ -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"/> @@ -107,9 +100,9 @@ <param argument="-p" name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/> <param argument="-ex_mode" name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" /> <param argument="-deCon" name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" /> - <param argument="-dense" name="dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" /> - <param argument="-ref_fsa" name="ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has 'n' instead of gaps" /> - <param argument="-matrix" name="matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Output assembly matrix" /> + <param argument="-dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" /> + <param argument="-ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has 'n' instead of gaps" /> + <param argument="-matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Output assembly matrix" /> <param argument="-a" name="all_best_mappings" type="boolean" truevalue="-a" falsevalue="" label="Print all best mappings" /> <param argument="-mp" name="minimum_phred_score" type="integer" min="0" value="20" max="60" label="Minimum phred score" /> <param argument="-5p" name="cut_5_prime" type="integer" min="0" value="0" max="64" label="Cut a constant number of nucleotides from the 5 prime" /> @@ -118,64 +111,149 @@ <param argument="-1t1" name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" /> <param argument="-bcd" name="base_call_depth" type="integer" min="1" value="1" max="1000" label="Minimum depth at base" /> <param argument="-mq" name="minimum_mapping_quality" type="integer" min="0" value="0" max="100" label="Minimum mapping quality" /> - <param argument="-reward" name="reward" type="integer" min="1" value="1" max="100" label="Score for match" /> - <param argument="-penalty" name="penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" /> - <param argument="-gapopen " name="gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" /> - <param argument="-gapextend" name="gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" /> + <param argument="-reward" type="integer" min="1" value="1" max="100" label="Score for match" /> + <param argument="-penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" /> + <param argument="-gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" /> + <param argument="-gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" /> <param argument="-per" name="pairing_reward" type="integer" min="1" value="7" max="100" label="Reward for pairing reads" /> <param argument="-cge" name="set_cge_penalties_and_rewards" type="boolean" truevalue="-cge" falsevalue="" label="Set CGE penalties and rewards" /> </when> </conditional> </inputs> <outputs> - <data name="result_overview" label="Result overview" format="tabular" from_work_dir="output.res" /> - <data name="consensus_alignment" label="Consensus alignment" format="fasta" from_work_dir="output.aln" /> - <data name="consensus_sequences" label="Consensus sequences" format="fasta" from_work_dir="output.fsa" /> - <data name="read_mapping" label="Read mapping info" format="tabular" from_work_dir="output.frag" /> - <data name="assembly_matrix" label="Assembly matrix" format="txt" from_work_dir="output.mat"> + <data name="result_overview" label="${tool.name} on ${on_string}: Result overview" format="tabular" from_work_dir="output.res" /> + <data name="consensus_alignment" label="${tool.name} on ${on_string}: Consensus alignment" format="txt" from_work_dir="output.aln" /> + <data name="consensus_sequences" label="${tool.name} on ${on_string}: Consensus sequences" format="fasta" from_work_dir="output.fsa" /> + <data name="read_mapping" label="${tool.name} on ${on_string}: Read mapping info" format="tabular" from_work_dir="output.frag" /> + <data name="assembly_matrix" label="${tool.name} on ${on_string}: Assembly matrix" format="tabular" from_work_dir="output.mat"> <filter>settings['matrix']</filter> </data> </outputs> <tests> - <test> - <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"/> + <test expect_num_outputs="4"> + <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> + <has_n_lines n="3"/> + <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="170"/> + <has_text text="b0842_1"/> + <has_text text="query" n="42"/> + <has_text text="template" n="42"/> + </assert_contents> + </output> + <output name="consensus_sequences" ftype="fasta"> + <assert_contents> + <has_line_matching expression="^>.*" n="2"/> + <has_line_matching expression="^>b0842_1"/> + </assert_contents> + </output> + <output name="read_mapping" ftype="tabular"> + <assert_contents> + <has_n_lines n="513"/> + <has_n_columns n="7"/> + <has_text text="b0842_1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="5"> + <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="result_overview" file="ERR884056.res" ftype="tabular"/> - <output name="consensus_alignment" file="ERR884056.aln" ftype="fasta"/> - <output name="consensus_sequences" file="ERR884056.fsa" ftype="fasta"/> - <output name="read_mapping" file="ERR884056.frag" ftype="tabular"/> + <output name="assembly_matrix" ftype="tabular"> + <assert_contents> + <has_n_lines n="2578"/> + <has_n_columns n="7" comment="#"/> + <has_line_matching expression="^A	.*"/> + <has_line_matching expression="^T	.*"/> + <has_line_matching expression="^C	.*"/> + <has_line_matching expression="^G	.*"/> + </assert_contents> + </output> </test> - <test> - <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"/> + <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="assembly_matrix" file="ERR884056.mat" ftype="txt"/> + <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="1048"/> + <has_n_columns n="7"/> + <has_text text="b0842_1"/> + </assert_contents> + </output> </test> </tests> - <help> - <![CDATA[ + <help><![CDATA[ When the mapping is done KMA will produce the following files: - *.res A result overview giving the most common statistics for each mapped template. - *.fsa The consensus sequences drawn from the alignments. - *.aln The consensus alignment of the reads against their template. - *.frag Mapping information on each mapped read, columns are: - 1. read - 2. number of equally well mapping templates - 3. mapping score - 4. start position - 5. end position (w.r.t. template) - 6. the choosen template. - *.mat Base counts on each position in each template, (only if “-matrix” is enabled) +* .res A result overview giving the most common statistics for each mapped template. +* .fsa The consensus sequences drawn from the alignments. +* .aln The consensus alignment of the reads against their template. +* .frag Mapping information on each mapped read, columns are: + 1. read + 2. number of equally well mapping templates + 3. mapping score + 4. start position + 5. end position (w.r.t. template) + 6. the choosen template. - ]]> - </help> +* .mat Base counts on each position in each template, (only if `-matrix` is enabled) +]]></help> <expand macro="citations" /> </tool>
--- a/macros.xml Sat Nov 27 09:35:27 2021 +0000 +++ b/macros.xml Mon Dec 15 21:59:27 2025 +0000 @@ -1,8 +1,8 @@ <macros> - <token name="@TOOL_VERSION@">1.2.21</token> - <token name="@INTYPES@"> - fastq,fastq.gz,fastqsanger,fastqsanger.gz - </token> + <token name="@TOOL_VERSION@">1.6.8</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</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">