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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper commit 20e805e46acfc9171da5e3281f3248295b6f8018
author nml
date Mon, 30 Dec 2024 17:58:09 +0000
parents 954b1b1ef3fb
children
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0:954b1b1ef3fb 1:4b4a7d9f7c9e
1 <tool id="ectyper" name="ectyper" version="1.0.0"> 1 <tool id="ectyper" name="ectyper" version="@VERSION@+galaxy0">
2 <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description> 2 <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description>
3 <xrefs> 3 <macros>
4 <token name="@VERSION@">2.0.0</token>
5 </macros>
6 <xrefs>
4 <xref type="bio.tools">ectyper</xref> 7 <xref type="bio.tools">ectyper</xref>
5 </xrefs> 8 </xrefs>
6 <requirements> 9 <requirements>
7 <requirement type="package" version="1.0.0">ectyper</requirement> 10 <requirement type="package" version="@VERSION@">ectyper</requirement>
8 </requirements> 11 </requirements>
9 <command detect_errors="exit_code"> 12 <command detect_errors="exit_code">
10 <![CDATA[ 13 <![CDATA[
11 #set $genomes = '' 14 #set $genomes = ''
12 #if hasattr($input, '__iter__') 15 #if hasattr($input, '__iter__')
46 49
47 #if $adv_param.mash_input 50 #if $adv_param.mash_input
48 --refseq mash_sketch.msh 51 --refseq mash_sketch.msh
49 #end if 52 #end if
50 53
54 #if $adv_param.pathotype
55 --pathotype
56 -pathpid $adv_param.pathotype_adv_param.pathpid
57 -pathpcov $adv_param.pathotype_adv_param.pathpcov
58 #end if
59
51 #if $adv_param.db_input 60 #if $adv_param.db_input
52 --dbpath custom_db.json 61 --dbpath custom_db.json
62 #end if
63
64 #if $adv_param.longreadsmode
65 --longreads
66 #end if
67
68 #if $adv_param.debugmode
69 --debug
53 #end if 70 #end if
54 71
55 --output '.' 72 --output '.'
56 ]]> 73 ]]>
57 </command> 74 </command>
58 <inputs> 75 <inputs>
59 <param name="input" type="data" format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s)"/> 76 <param name="input" type="data" format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s)"/>
60 <section name="adv_param" title="Advanced parameters" expanded="False"> 77 <section name="adv_param" title="Advanced parameters" expanded="False">
61 <param name="opid" label="O antigen minimum %identity" type="integer" value="90" min="1" max="100"/> 78 <param name="opid" label="O antigen minimum %identity" type="integer" value="95" min="1" max="100"/>
62 <param name="opcov" label="O antigen minimum %coverage" type="integer" value="90" min="1" max="100"/> 79 <param name="opcov" label="O antigen minimum %coverage" type="integer" value="90" min="1" max="100"/>
63 <param name="hpid" label="H antigen minimum %identity" type="integer" value="95" min="1" max="100"/> 80 <param name="hpid" label="H antigen minimum %identity" type="integer" value="95" min="1" max="100"/>
64 <param name="hpcov" label="H antigen minimum %coverage" type="integer" value="50" min="1" max="100"/> 81 <param name="hpcov" label="H antigen minimum %coverage" type="integer" value="50" min="1" max="100"/>
65 <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/> 82 <param name="verifyEcoli" type="boolean" checked="false" label="Enable E. coli species and results QC verification"/>
66 <param name="blastresults" type="boolean" checked="false" label="Include BLAST allele alignment results tab-delim file in the outputs?" /> 83 <param name="blastresults" type="boolean" checked="false" label="Include BLAST allele alignment results tab-delim file in the outputs?" />
67 <param name="logging" type="boolean" checked="false" label="Include log file in the run outputs?" /> 84 <param name="logging" type="boolean" checked="false" label="Include log file in the run outputs?" />
68 <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide custom MASH genome sketch to help with species identification (otherwise default RefSeq sketch is used)"/> 85 <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide custom MASH genome sketch to help with species identification (otherwise default RefSeq sketch is used)"/>
69 <param name="db_input" type="data" optional="true" format="json" label="Custom database of alleles (Optional)" help="Optionally provide custom database of alleles in JSON format"/> 86 <param name="pathotype" type="boolean" checked="true" label="Enable E.coli pathotyping and Shiga toxin (stx) subtyping (Recommended)"/>
87 <section name="pathotype_adv_param" title="Advanced parameters (pathoyping and shiga toxin subtyping)" expanded="False">
88 <param name="pathpid" label="Minimum %identity required for a pathotype/toxin database reference allele match" type="integer" value="90" min="1" max="100"/>
89 <param name="pathpcov" label="Minimum %coverage required for a pathotype/toxin database reference allele match" type="integer" value="50" min="1" max="100"/>
90 </section>
91 <param name="longreadsmode" type="boolean" checked="false" label="Enable long read mapping mode (Optional)" help="Enable this mode if no typing results are obtained"/>
92 <param name="db_input" type="data" optional="true" format="json" label="Custom database of O and H antigen alleles (Optional)" help="Optionally provide custom database of alleles in JSON format"/>
93 <param name="debugmode" type="boolean" checked="false" label="Enable debug mode with high log messages verbosity"/>
70 </section> 94 </section>
71 </inputs> 95 </inputs>
72 <outputs> 96 <outputs>
73 <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report on ${input.element_identifier}"> </data> 97 <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report on ${input.element_identifier}"> </data>
74 <data name="output_log" format="txt" from_work_dir="ectyper.log" label="${tool.name} log file on ${input.element_identifier}"> 98 <data name="output_log" format="txt" from_work_dir="ectyper.log" label="${tool.name} log file on ${input.element_identifier}">
78 <filter>adv_param['blastresults']==True</filter> 102 <filter>adv_param['blastresults']==True</filter>
79 </data> 103 </data>
80 </outputs> 104 </outputs>
81 <tests> 105 <tests>
82 <test expect_num_outputs="1"> 106 <test expect_num_outputs="1">
83 <param name="input" value="Escherichia2.fastq"/> 107 <param name="input" value="Escherichia2.fastq" ftype="fastq"/>
84 <assert_stderr>
85 <has_text text="O22"/>
86 <has_text text="H8"/>
87 </assert_stderr>
88 <output name="output_result" ftype="tabular" > 108 <output name="output_result" ftype="tabular" >
89 <assert_contents> 109 <assert_contents>
90 <has_text_matching expression="O22"/> 110 <has_text_matching expression="O22"/>
111 <has_text text="H8"/>
91 </assert_contents> 112 </assert_contents>
92 </output> 113 </output>
93 </test> 114 </test>
115 <test expect_num_outputs="1">
116 <param name="input" value="Escherichia1.fasta" ftype="fasta"/>
117 <output name="output_result" ftype="tabular">
118 <assert_contents>
119 <has_text text="O103:H2"/>
120 <has_text text="EHEC-STEC"/>
121 <has_text text="stx1a;stx2a"/>
122 <has_text text="eae,ehxA,hlyE,stx1,stx2"/>
123 </assert_contents>
124 </output>
125 </test>
94 </tests> 126 </tests>
95 127
96 <help> 128 <help>
97 **Syntax** 129 **Syntax**
98 130