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comparison fargene.xml @ 2:b982a9ea939c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
author iuc
date Fri, 09 Feb 2024 21:30:09 +0000
parents 239ce9f24386
children
comparison
equal deleted inserted replaced
1:239ce9f24386 2:b982a9ea939c
1 <tool id="fargene" name="fargene" version="@VERSION@+galaxy1"> 1 <tool id="fargene" name="fargene" version="@VERSION@+galaxy1">
2 <description>Fragmented antibiotic resistance gene identifier </description> 2 <description>Fragmented antibiotic resistance gene identifier </description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <xrefs>
7 <xref type="bio.tools">fargene</xref>
8 </xrefs>
6 <expand macro="requirements" /> 9 <expand macro="requirements" />
7 <version_command>fargene --version</version_command> 10 <version_command>fargene --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
9 #import re 12 #import re
10 #if $inputs.input_type == 'paired': 13 #if $inputs.input_type == 'paired':
100 <option value="class_c">Class C beta-lactamases</option> 103 <option value="class_c">Class C beta-lactamases</option>
101 <option value="class_d_1">Class D beta-lactamases-1</option> 104 <option value="class_d_1">Class D beta-lactamases-1</option>
102 <option value="class_d_2">Class D beta-lactamases-2</option> 105 <option value="class_d_2">Class D beta-lactamases-2</option>
103 <option value="qnr">QNR</option> 106 <option value="qnr">QNR</option>
104 </param> 107 </param>
105 <param name="score" argument="--score" type="float" value="0.0" label="The threshold score for a sequence to be classified as 108 <param argument="--score" type="float" value="0.0" label="The threshold score for a sequence to be classified as a (almost) complete gene" />
106 a (almost) complete gene" /> 109 <param argument="--meta-score" type="float" value="0.0" label="The threshold score for a fragment to be classified as a positive. Expressed as score per amino acid" />
107 <param name="meta_score" argument="--meta-score" type="float" value="0.0" label="The threshold score for a fragment to be classified as 110 <param argument="--protein" type="boolean" truevalue="--protein" falsevalue="" checked="False" label="Rescue short unassmebled plasmids" />
108 a positive. Expressed as score per amino acid" /> 111 <param argument="--min-orf-length" type="integer" min="1" value="90" label="The minimal length for a retrieved predicted ORF (nt)" />
109 <param name="protein" argument="--protein" type="boolean" truevalue="--protein" falsevalue="" checked="False" label="Rescue short unassmebled plasmids" /> 112 <param argument="--retrieve-whole" type="boolean" truevalue="--retrieve-whole " falsevalue="" checked="False" label="Use this flag if the whole sequence where a hit is detected should be retrieved" />
110 <param name="min_orf_length" argument="--min-orf-length" type="integer" min="1" value="90" label="The minimal length for a retrieved predicted ORF (nt)" /> 113 <param argument="--no-orf-predict" type="boolean" truevalue="--no-orf-predict" falsevalue="" checked="False" label="Do not perform ORF prediction" />
111 <param name="retrieve_whole" argument="--retrieve-whole" type="boolean" truevalue="--retrieve-whole " falsevalue="" checked="False" label="Use this flag if the whole sequence where a hit is 114 <param argument="--no-quality-filtering" type="boolean" truevalue="--no-quality-filtering" falsevalue="" checked="False" label="Use if no quality control should be performed on the metagenomic data" />
112 detected should be retrieved" /> 115 <param argument="--no-assembly" type="boolean" truevalue="--no-assembly" falsevalue="" checked="False" label="Use if you want to skip the assembly and retrieval of contigs for metagenomic data" />
113 <param name="no_orf_predict" argument="--no-orf-predict" type="boolean" truevalue="--no-orf-predict" falsevalue="" checked="False" label="Do not perform ORF prediction" /> 116 <param argument="--orf-finder" type="boolean" truevalue="--orf-finder" falsevalue="" checked="False" label="Use NCBI ORFfinder instead of prodigal for ORF prediction of genomes/contigs" />
114 <param name="no_quality_filtering" argument="--no-quality-filtering" type="boolean" truevalue="--no-quality-filtering" falsevalue="" checked="False" label="Use if no quality control should be performed on the 117 <param argument="--store-peptides" type="boolean" truevalue="--store-peptides" falsevalue="" checked="False" label="Store the translated sequences"
115 metagenomic data" /> 118 help="Useful if you plan to redo the analysis using a different model and want to skip the preprocessing steps" />
116 <param name="no_assembly" argument="--no-assembly" type="boolean" truevalue="--no-assembly" falsevalue="" checked="False" label="Use if you want to skip the assembly and retrieval of
117 contigs for metagenomic data" />
118 <param name="orf_finder" argument="--orf-finder" type="boolean" truevalue="--orf-finder" falsevalue="" checked="False" label="Use NCBI ORFfinder instead of prodigal for ORF
119 prediction of genomes/contigs" />
120 <param name="store_peptides" argument="--store-peptides" type="boolean" truevalue="--store-peptides" falsevalue="" checked="False" label="Store the translated sequences. Useful if you plan to
121 redo the analysis using a different model and want to
122 skip the preprocessing steps" />
123 119
124 </inputs> 120 </inputs>
125 <outputs> 121 <outputs>
126 <data name="summary" format="txt" from_work_dir="fargene_output/results_summary.txt" label="${tool.name} on ${on_string} (Summary)"> 122 <data name="summary" format="txt" from_work_dir="fargene_output/results_summary.txt" label="${tool.name} on ${on_string} (Summary)">
127 </data> 123 </data>