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comparison mob_typer.xml @ 11:179497074102 draft default tip

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite commit bc53cd0c79b976fc17f854ede446e61d6c9bb49a
author nml
date Wed, 26 Feb 2025 15:14:46 +0000
parents 2fd93022d5d7
children
comparison
equal deleted inserted replaced
10:2fd93022d5d7 11:179497074102
1 <tool id="mob_typer" name="MOB-Typer" version="@VERSION@+galaxy0"> 1 <tool id="mob_typer" name="MOB-Typer" version="@VERSION@+galaxy1">
2 <description>Get the plasmid type and mobility given its sequence</description> 2 <description>Get the plasmid type and mobility given its sequence</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
63 #end if 63 #end if
64 64
65 #if $adv_param.biomarker_report_file 65 #if $adv_param.biomarker_report_file
66 --biomarker_report_file biomarker_report.txt 66 --biomarker_report_file biomarker_report.txt
67 #end if 67 #end if
68 68
69
70 --out_file plasmid_report.txt; 69 --out_file plasmid_report.txt;
71 70
72 ]]> 71 ]]>
73 </command> 72 </command>
74 <inputs> 73 <inputs>
75 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> 74 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
76 <section name="adv_param" title="Advanced parameters" expanded="False"> 75 <section name="adv_param" title="Advanced parameters" expanded="False">
77 <param name="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independent plasmid?" help="Treat each sequence in the FASTA file as a separate input (--multi)" /> 76 <param name="multi" type="boolean" checked="false" label="Treat each input sequence as an independent plasmid?" help="Treat each sequence in the FASTA file as a separate input (--multi)" />
78 <param name="biomarker_report_file" type="boolean" truevalue="true" falsevalue="" checked="false" label="Output BLAST biomarker report?" help="The report will report all biomarkers identified in a given query plasmid (--biomarker_report_file)" /> 77 <param name="biomarker_report_file" type="boolean" checked="true" label="Output BLAST biomarker report?" help="The report will report all biomarkers identified in a given query plasmid (--biomarker_report_file)" />
79
80 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn" help="(--min_rep_evalue)"/> 78 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn" help="(--min_rep_evalue)"/>
81 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn" help="(--min_mob_evalue)"/> 79 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn" help="(--min_mob_evalue)"/>
82 <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn" help="(--min_con_evalue)"/> 80 <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn" help="(--min_con_evalue)"/>
83 <param name="min_length" type="integer" value="1000" label="Minimum length of contigs to classify (bp)" help="(--min_length)"/> 81 <param name="min_length" type="integer" value="1000" label="Minimum length of contigs to classify (bp)" help="(--min_length)"/>
84 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80" help="(--min_rep_ident)"/> 82 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80" help="(--min_rep_ident)"/>
99 <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help="FASTA of known plasmid oriT DNA sequences custom database (--plasmid_orit)"/> 97 <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help="FASTA of known plasmid oriT DNA sequences custom database (--plasmid_orit)"/>
100 </section> 98 </section>
101 </inputs> 99 </inputs>
102 <outputs> 100 <outputs>
103 <data name="plasmid_report" from_work_dir="plasmid_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}" format="tabular" /> 101 <data name="plasmid_report" from_work_dir="plasmid_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}" format="tabular" />
104 <data name="biomarker_report" from_work_dir="biomarker_report.txt" label="${tool.name}: Biomarker report on ${input.element_identifier}" format="tabular" /> 102 <data name="biomarker_report" from_work_dir="biomarker_report.txt" label="${tool.name}: Biomarker report on ${input.element_identifier}" format="tabular">
103 <filter>adv_param["biomarker_report_file"]</filter>
104 </data>
105 </outputs> 105 </outputs>
106 <tests> 106 <tests>
107 <test> 107 <test expect_num_outputs="2">
108 <param name="input" value="plasmid_476.fasta" ftype="fasta"/> 108 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
109 <output name="plasmid_report"> 109 <output name="plasmid_report">
110 <assert_contents> 110 <assert_contents>
111 <has_text text="KJ484639"/> 111 <has_text text="KJ484639"/>
112 <has_text text="MOBP"/> 112 <has_text text="MOBP"/>