| Previous changeset 3:e8405163fb4e (2021-08-10) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a" |
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modified:
macro.xml mykrobe_predict.xml |
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| diff -r e8405163fb4e -r a2e3ad69ee23 macro.xml --- a/macro.xml Tue Aug 10 11:29:58 2021 +0000 +++ b/macro.xml Thu Aug 26 20:38:36 2021 +0000 |
| [ |
| b'@@ -1,121 +1,102 @@\n-<?xml version="1.1"?>\n <macros>\n- <token name="@TOOL_VERSION@">0.10.0</token>\n- <xml name="requirements">\n- <requirements>\n- <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement>\n- </requirements> \n- </xml>\n- <token name="@select_inputs@">\n- <![CDATA[\n- #set $name=\'sample\'\n- ]]>\n- </token>\n-\n- <token name="@shared_options@">\n- <![CDATA[\n- #if $kmer:\n- --kmer \'${kmer}\'\n- #end if\n- #if $expected_depth:\n- --expected_depth \'${expected_depth}\'\n- #end if\n-\n- $ont\n-\n- $report_all_calls\n+ <token name="@TOOL_VERSION@">0.10.0</token>\n+ <token name="@PROFILE@">20.09</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement>\n+ </requirements>\n+ </xml>\n \n- #if $expected_error_rate:\n- --expected_error_rate \'${expected_error_rate}\'\n- #end if\n-\n- #if $min_variant_conf:\n- --min_variant_conf \'${min_variant_conf}\'\n- #end if\n-\n- #if $min_gene_conf:\n- --min_gene_conf \'${min_gene_conf}\'\n- #end if\n-\n- #if $min_proportion_expected_depth:\n- --min_proportion_expected_depth \'${min_proportion_expected_depth}\'\n- #end if\n-\n- #if $min_gene_percent_covg_threshold:\n- --min_gene_percent_covg_threshold \'${min_gene_percent_covg_threshold}\'\n- #end if\n-\n- $guess_sequence_method\n-\n- $ignore_minor_calls\n-\n- #if $ignore_filtered:\n- --ignore_filtered \'${ignore_filtered}\'\n- #end if\n-\n- #if $model:\n- --model \'${model}\'\n- #end if\n+ <token name="@shared_options@">\n+ <![CDATA[\n+ #if $kmer:\n+ --kmer ${kmer}\n+ #end if\n+ #if $expected_depth:\n+ --expected_depth ${expected_depth}\n+ #end if\n+ $ont\n+ $report_all_calls\n+ #if $expected_error_rate:\n+ --expected_error_rate ${expected_error_rate}\n+ #end if\n+ #if $min_variant_conf:\n+ --min_variant_conf ${min_variant_conf}\n+ #end if\n+ #if $min_gene_conf:\n+ --min_gene_conf ${min_gene_conf}\n+ #end if\n+ #if $min_proportion_expected_depth:\n+ --min_proportion_expected_depth ${min_proportion_expected_depth}\n+ #end if\n+ #if $min_gene_percent_covg_threshold:\n+ --min_gene_percent_covg_threshold ${min_gene_percent_covg_threshold}\n+ #end if\n+ $guess_sequence_method\n+ $ignore_minor_calls\n+ #if $ignore_filtered:\n+ --ignore_filtered \'${ignore_filtered}\'\n+ #end if\n+ #if $model:\n+ --model \'${model}\'\n+ #end if\n+ #if $ploidy:\n+ --ploidy \'${ploidy}\'\n+ #end if\n+ ]]>\n+ </token>\n \n- #if $ploidy:\n- --ploidy \'${ploidy}\'\n- #end if\n- ]]>\n- </token>\n-\n- <xml name="inputs">\n- <conditional name="data_type">\n- <param name="type" type="select" label="Specify the read type.">\n- <option value="single">Single-end Data</option>\n- <option value="paired">Paired-end Data</option>\n- <option value="collection">Collection Paired-end Data</option>\n- </param>\n- <when value="single">\n- <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/>\n- </when>\n- <when value="paired">\n- <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/>\n- <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/>\n- </when>\n- <when value="collection">\n- '..b'inor calls when running resistance prediction"/>\n- <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don\'t include filtered genotypes"/>\n- <param argument="--guess_sequence_method" type="boolean" truevalue="--guess_sequence_method" falsevalue="" label="Guess sequence method" help="Guess if ONT or Illumia based on error rate. If error rate is > 10%, ploidy is set to haploid and a confidence threshold is used"/>\n- </xml>\n+ <xml name="options">\n+ <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>\n+ <param argument="--expected_error_rate" optional="True" type="float" label="Expected error rate" help="Expected sequencing error rate. Set to 0.15 for ONT genotyping"/>\n+ <param argument="--expected_depth" optional="True" type="integer" min="0" label="Expected depth" help=""/>\n+ <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data" help=""/>\n+ <param argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping" help=""/>\n+ <param argument="--min_gene_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for gene genotyping" help=""/>\n+ <param argument="--min_gene_percent_covg_threshold" optional="True" type="integer" min="0" label="Minimum gene predict coverage" help="all genes alleles found above this percent coverage will be reported (default 100 (only best alleles reported))"/>\n+ <param argument="--min_proportion_expected_depth" optional="True" type="float" label="Minimum depth required on the sum of both alleles" help="Default 0.3 (30%)"/>\n+ <param argument="--model" optional="True" type="data" format="txt" label="Genotype model used" help="default kmer_count. Options kmer_count, median_depth"/>\n+ <param argument="--ploidy" optional="True" type="select" label="Diploid or Haploid" help="Use a diploid (includes 0/1 calls) or haploid genotyping model">\n+ <option value="diploid">diploid</option>\n+ <option value="haploid">haploid</option>\n+ </param>\n+ <param argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="Report all calls" help=""/>\n+ <param argument="--ignore_minor_calls" type="boolean" truevalue="--ignore_minor_calls" falsevalue="" label="Ignore minor calls" help="Ignore minor calls when running resistance prediction"/>\n+ <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don\'t include filtered genotypes"/>\n+ <param argument="--guess_sequence_method" type="boolean" truevalue="--guess_sequence_method" falsevalue="" label="Guess sequence method" help="Guess if ONT or Illumia based on error rate. If error rate is > 10%, ploidy is set to haploid and a confidence threshold is used"/>\n+ </xml>\n \n- <token name="@ATTRIBUTION@">\n- <![CDATA[\n- \n- **MyKrobe predict - Antibiotic resistance predictions**\n- \n- Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis\n- using Bruijn graph.\n- ]]> \n- </token>\n+ <token name="@ATTRIBUTION@">\n+ <![CDATA[\n+ **MyKrobe predict - Antibiotic resistance predictions**\n+ Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis\n+ using Bruijn graph.\n+ ]]>\n+ </token>\n \n- <xml name="citation">\n- <citations>\n- <citation type="doi">10.1038/ncomms10063</citation>\n- </citations>\n- </xml>\n+ <xml name="citation">\n+ <citations>\n+ <citation type="doi">10.1038/ncomms10063</citation>\n+ </citations>\n+ </xml>\n </macros>\n' |
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| diff -r e8405163fb4e -r a2e3ad69ee23 mykrobe_predict.xml --- a/mykrobe_predict.xml Tue Aug 10 11:29:58 2021 +0000 +++ b/mykrobe_predict.xml Thu Aug 26 20:38:36 2021 +0000 |
| [ |
| b'@@ -1,129 +1,140 @@\n-<tool id="mykrobe_predict" name="mkyrobe predict" version="@TOOL_VERSION@">\n- <description>Antibiotic resistance predictions</description>\n- <macros>\n- <import>macro.xml</import>\n- </macros>\n- <expand macro="requirements"/>\n- <command detect_errors="exit_code">\n-<![CDATA[\n- @select_inputs@\n+<tool id="mykrobe_predict" name="mkyrobe predict" version="@TOOL_VERSION@.1+galaxy0" profile="@PROFILE@">\n+ <description>Antibiotic resistance predictions</description>\n+ <macros>\n+ <import>macro.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+#import difflib\n+#import re\n \n- mykrobe predict \n- --sample \'${name}\'\n- --species ${select_species.species}\n- --panel \'${select_species.panel}\'\n+mykrobe predict\n+--species \'${select_species.species}\'\n+--panel \'${select_species.panel}\'\n \n- #if $conf_percent_cutoff:\n- --conf_percent_cutoff \'${conf_percent_cutoff}\'\n- #end if\n+#if $conf_percent_cutoff:\n+ --conf_percent_cutoff \'${conf_percent_cutoff}\'\n+#end if\n \n- #if $min_depth:\n- --min_depth \'${min_depth}\'\n- #end if\n+#if $min_depth:\n+ --min_depth ${min_depth}\n+#end if\n \n- @shared_options@\n+@shared_options@\n \n- -q\n- -t "\\${GALAXY_SLOTS:-1}"\n+-q\n+-t "\\${GALAXY_SLOTS:-1}"\n \n- --seq\n- #if $data_type.type == "single":\n- $data_type.seq1\n- #elif $data_type.type == "paired":\n-\t $data_type.seq1 $data_type.seq2\n- #elif $data_type.type == "collection":\n- $data_type.collection1.forward $data_type.collection1.reverse\n-\t#end if\n+#if $data_type.type in ["single", "paired"]:\n+ #set read1 = $data_type.seq1\n+ #set read1_identifier = re.sub(\'[^\\s\\w\\-]\', \'_\', str($read1.element_identifier))\n+ #if $data_type.type == "single":\n+ --sample \'${read1_identifier}\'\n+ --seq \'${read1}\'\n+ #else:\n+ #set read2 = $data_type.seq2\n+ #set read2_identifier = re.sub(\'[^\\s\\w\\-]\', \'_\', str($read2.element_identifier))\n+ #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks()\n+ #set match = $matches[0]\n+ #set identifier = re.sub(\'[^\\s\\w\\-]\', \'_\', str($read1_identifier[match.a:match.a + match.size]))\n+ --sample \'${identifier}\'\n+ --seq \'${read1}\' \'${read2}\'\n+ #end if\n+#elif $data_type.type == "collection":\n+ #set identifier = re.sub(\'[^\\s\\w\\-]\', \'_\', str($data_type.collection1.element_identifier))\n+ --sample \'${identifier}\'\n+ --seq \'${data_type.collection1.forward}\' \'${data_type.collection1.reverse}\'\n+#end if\n \n- --format \'${format}\'\n+--format \'${format}\'\n \n- > \'$output\'\n-]]>\n- </command>\n- <inputs>\n- <expand macro="inputs"/>\n- <conditional name="select_species">\n- <param name="species" type="select" label="Specify Species for AMR">\n- <option value="tb">Mycobacterium tuberculosis (tb)</option>\n- <option value="staph">Staphylococcus aureus (staph)</option>\n- <option value="sonnei">Shigella sonnei (sonnei)</option>\n- </param>\n- <when value="staph">\n- <param name="panel" type="select" label="Select panel for Staph only">\n- <option value="20170217">20170217</option>\n- </param>\n- </when>\n- <when value="tb">\n-\t<param name="panel" type="select" label="Select panel for TB only">\n- <option value="202010">202010</option>\n- <option value="201901">201901</option>\n- <option value="bradley-2015">Bradely 2015</option>\n+> \'$output\']]>\n+ </command>\n+ <inputs>\n+ <expand macro="inputs"/>\n+ <conditional name="select_species">\n+ <param name="species" type="select" label="Specify Species for AMR">\n+ <option value="tb">Mycobacterium tuberculosis (tb)</option>\n+ <option value="staph">Staphylococcus aureus (staph)</option>\n+ <option value="sonnei">Shig'..b't_conf, by simulating variants and choosing the cutoff that would keep x% of the variants. Default is 90 if --ont, otherwise --min_variant_conf is used as the cutoff">\n- <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" />\n- </param>\n- <expand macro="options"/>\n- <param argument="--format" type="select" label="Select the prefered output format">\n- <option value="csv" >csv</option>\n- <option value="json">json</option>\n- </param>\n- </inputs>\n- <outputs>\n- <data name="output" format="csv" label="prediction">\n- <change_format>\n- <when input="format" value="json" format="json"/>\n- </change_format>\n- </data>\n- </outputs>\n- <tests>\n- <test>\n- <param name="type" value="single"/>\n- <param name="seq1" ftype="fastq" value="reads.fastq"/>\n- <param name="species" value="tb"/>\n- <param name="panel" value="bradley-2015"/>\n- <param name="format" value="json"/>\n- <output name="output">\n- <assert_contents>\n- <has_text_matching expression="susceptibility"/>\n- </assert_contents>\n- </output>\n- </test>\n- <test>\n- <param name="type" value="single"/>\n- <param name="seq1" ftype="fastq" value="reads.fastq"/>\n- <param name="species" value="sonnei"/>\n- <param name="panel" value="20201012"/>\n- <param name="format" value="json"/>\n- <output name="output">\n- <assert_contents>\n- <has_text_matching expression="susceptibility"/>\n- </assert_contents>\n- </output>\n- </test>\n- <test>\n- <param name="type" value="single"/>\n- <param name="seq1" ftype="fastq.gz" value="reads.fastq.gz"/>\n- <param name="species" value="sonnei"/>\n- <param name="panel" value="20201012"/>\n- <param name="format" value="json"/>\n- <output name="output">\n- <assert_contents>\n- <has_text_matching expression="susceptibility"/>\n- </assert_contents>\n- </output>\n- </test>\n- </tests>\n- <help>\n- @ATTRIBUTION@\n- </help>\n- <expand macro="citation" />\n+ </inputs>\n+ <outputs>\n+ <data name="output" format="csv" label="prediction">\n+ <change_format>\n+ <when input="format" value="json" format="json"/>\n+ </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="type" value="single"/>\n+ <param name="seq1" ftype="fastq" value="reads.fastq"/>\n+ <param name="species" value="tb"/>\n+ <param name="panel" value="bradley-2015"/>\n+ <param name="format" value="json"/>\n+ <output name="output">\n+ <assert_contents>\n+ <has_text_matching expression="susceptibility"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="type" value="single"/>\n+ <param name="seq1" ftype="fastq" value="reads.fastq"/>\n+ <param name="species" value="sonnei"/>\n+ <param name="panel" value="20201012"/>\n+ <param name="format" value="json"/>\n+ <output name="output">\n+ <assert_contents>\n+ <has_text_matching expression="susceptibility"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="type" value="single"/>\n+ <param name="seq1" ftype="fastq.gz" value="reads.fastq.gz"/>\n+ <param name="species" value="sonnei"/>\n+ <param name="panel" value="20201012"/>\n+ <param name="format" value="json"/>\n+ <output name="output">\n+ <assert_contents>\n+ <has_text_matching expression="susceptibility"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+ @ATTRIBUTION@\n+ </help>\n+ <expand macro="citation" />\n </tool>\n+\n' |