| Previous changeset 1:7c2f5268d01c (2020-10-09) Next changeset 3:15200570e926 (2021-11-21) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty commit de6983a7051906335902c024710783551912d292" |
|
modified:
novoplasty.xml |
| b |
| diff -r 7c2f5268d01c -r 64a1c751d99b novoplasty.xml --- a/novoplasty.xml Fri Oct 09 17:45:30 2020 +0000 +++ b/novoplasty.xml Sun Jul 18 10:34:40 2021 +0000 |
| [ |
| b'@@ -3,7 +3,7 @@\n <description>de novo assembler for short circular genomes</description>\n <macros>\n <token name="@TOOL_VERSION@">4.2</token>\n- <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n <xml name="content" token_min="" token_max="">\n <param name="genome_range_min" type="text" value="@MIN@" label="Set lower limit for the expected genome size range" help="(Genome Range)"/>\n <param name="genome_range_max" type="text" value="@MAX@" label="Set upper limit for the expected genome size range" help="(Genome Range)"/>\n@@ -34,42 +34,52 @@\n Project:\n -----------------------\n Project name = result\n-Type = ${type_cond.type_sel}\n-Genome Range = ${type_cond.genome_range_min}-${type_cond.genome_range_max}\n-K-mer = ${kmer}\n+Type = ${assembly_options.type_cond.type_sel}\n+Genome Range = ${assembly_options.type_cond.genome_range_min}-${assembly_options.type_cond.genome_range_max}\n+K-mer = ${assembly_options.kmer}\n Max memory = \n Extended log = 1\n-Save assembled reads = ${save_assembled_reads}\n+Save assembled reads = ${optional.save_assembled_reads}\n Seed Input = ${seed_input}\n-Extend seed directly = ${extend_seed_directly}\n-Reference sequence = #if $reference then $reference else \'\'#\n-Variance detection = #if $platform_cond.platform_sel == \'illumina\' and $platform_cond.mode_cond.mode_sel == \'variance\' then \'yes\' else \'\'#\n-Heteroplasmy = \n-MAF = #if $platform_cond.platform_sel == \'illumina\' and $platform_cond.mode_cond.mode_sel == \'heteroplasmy\' then $platform_cond.mode_cond.maf else \'\'#\n-HP exclude list = \n-Chloroplast sequence = #if $type_cond.type_sel == \'mito_plant\' and $type_cond.chloroplast_sequence then $type_cond.chloroplast_sequence else \'\'#\n+Extend seed directly = ${assembly_options.extend_seed_directly}\n+Reference sequence = #if $reference_cond.use_reference == \'true\' and $reference_cond.reference then $reference_cond.reference else \'\'#\n+Variance detection = #if $reference_cond.use_reference == \'true\' then $reference_cond.variance_detection else \'\'#\n+Chloroplast sequence = #if $assembly_options.type_cond.type_sel == \'mito_plant\' and $assembly_options.type_cond.chloroplast_sequence then $assembly_options.type_cond.chloroplast_sequence else \'\'#\n \n Dataset 1:\n -----------------------\n-Read Length = ${read_length}\n-Insert size = ${insert_size}\n-Platform = ${$platform_cond.platform_sel}\n-Single/Paired = ${single_paired}\n+Read Length = ${read_options.read_length}\n+Insert size = ${read_options.insert_size}\n+Platform = ${read_options.platform}\n+Single/Paired = PE\n Combined reads = #if $reads_cond.reads_sel == \'combined\' then \'combined.\'+$reads_cond.combined_reads.datatype.file_ext else \'\'#\n Forward reads = #if $reads_cond.reads_sel == \'separate\' then \'forward.\'+$reads_cond.forward_reads.datatype.file_ext else \'\'#\n Reverse reads = #if $reads_cond.reads_sel == \'separate\' then \'reverse.\'+$reads_cond.reverse_reads.datatype.file_ext else \'\'#\n \n+Heteroplasmy:\n+-----------------------\n+MAF = #if $reference_cond.use_reference == \'true\' and $reference_cond.heteroplasmy_cond.detect_heteroplasmy == \'true\' then $reference_cond.heteroplasmy_cond.maf else \'\'#\n+HP exclude list = ## option not available\n+PCR-free = #if $reference_cond.use_reference == \'true\' and $reference_cond.heteroplasmy_cond.detect_heteroplasmy == \'true\' then $reference_cond.heteroplasmy_cond.pcr_free else \'\'#\n+\n Optional:\n -----------------------\n-Insert size auto = ${insert_size_auto}\n-Use Quality Scores = ${use_quality_scores}\n+Insert size auto = ${optional.insert_size_auto}\n+Insert Range = ${optional.insert_range}\n+Insert Range strict = ${optional.'..b'#009;FILTER	INFO"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_ha">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_lth">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_pn">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_pna">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_ltn">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_cm">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_cl">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- #9 Test insert range options -->\n+ <test expect_num_outputs="6">\n+ <conditional name="reads_cond">\n+ <param name="reads_sel" value="separate"/>\n+ <param name="forward_reads" value="forward.fasta.gz"/>\n+ <param name="reverse_reads" value="reverse.fasta.gz"/>\n+ </conditional>\n+ <section name="assembly_options">\n+ <conditional name="type_cond">\n+ <param name="type_sel" value="mito"/>\n+ </conditional>\n+ </section>\n+ <section name="optional">\n+ <param name="insert_range" value="1.9"/>\n+ <param name="insert_range_strict" value="1.3"/>\n+ </section> \n+ <!-- fasta.gz not supported -->\n+ <param name="seed_input" value="seed.fasta"/>\n+ <!-- Assembly -->\n+ <output name="out_c">\n+ <assert_contents>\n <has_n_lines n="110"/>\n </assert_contents>\n </output>\n+ <output name="out_ct">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_ua">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- #10 Test save assembled reads option -->\n+ <test expect_num_outputs="8">\n+ <conditional name="reads_cond">\n+ <param name="reads_sel" value="separate"/>\n+ <param name="forward_reads" value="forward.fasta.gz"/>\n+ <param name="reverse_reads" value="reverse.fasta.gz"/>\n+ </conditional>\n+ <section name="assembly_options">\n+ <conditional name="type_cond">\n+ <param name="type_sel" value="mito"/>\n+ </conditional>\n+ </section>\n+ <section name="optional">\n+ <param name="save_assembled_reads" value="true"/>\n+ </section>\n+ <!-- fasta.gz not supported -->\n+ <param name="seed_input" value="seed.fasta"/>\n+ <!-- Assembly -->\n+ <output name="out_c">\n+ <assert_contents>\n+ <has_n_lines n="110"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_ua">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n <help><![CDATA[\n' |