annotate fargene.xml @ 2:b982a9ea939c draft default tip

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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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239ce9f24386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 0b2de0d35b6ef4c0ef0dd77e8415115a4a3b415b"
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1 <tool id="fargene" name="fargene" version="@VERSION@+galaxy1">
0
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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2 <description>Fragmented antibiotic resistance gene identifier </description>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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3 <macros>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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4 <import>macros.xml</import>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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5 </macros>
2
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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6 <xrefs>
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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7 <xref type="bio.tools">fargene</xref>
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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8 </xrefs>
0
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9 <expand macro="requirements" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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10 <version_command>fargene --version</version_command>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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11 <command detect_errors="exit_code"><![CDATA[
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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12 #import re
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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13 #if $inputs.input_type == 'paired':
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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14 #set $safename_R1 = re.sub('[^\w\-_\.]', '_', $inputs.R1.element_identifier)
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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15 #set $safename_R2 = re.sub('[^\w\-_\.]', '_', $inputs.R2.element_identifier)
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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16 ln -fs '$inputs.R1' ${safename_R1}.fastq &&
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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17 ln -fs '$inputs.R2' ${safename_R2}.fastq &&
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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18 #elif $inputs.input_type == 'collection':
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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19 #for $i, $input in enumerate($inputs.input_collection)
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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20 #set $safename_fwd = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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21 ln -fs '${input.forward}' ${safename_fwd}_1.fastq &&
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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22 #set $safename_rvs = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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23 ln -fs '${input.reverse}' ${safename_rvs}_2.fastq &&
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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24 #end for
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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25 #elif $inputs.input_type == 'sequence':
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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26 #for $input in $inputs.input_sequence
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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27 #set $safename_seq = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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28 ln -fs '$input' ${safename_seq}.fasta &&
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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29 #end for
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30 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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31
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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32 fargene
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33 --infiles
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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34 #if $inputs.input_type in ('paired', 'collection'):
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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35 *.fastq
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36 --meta
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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37 #elif $inputs.input_type == 'sequence':
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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38 *.fasta
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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39 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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40 --hmm-model $models
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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41 --output fargene_output
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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42 --tmp-dir tmp
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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43 -p \${GALAXY_SLOTS:-4}
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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44 #if $meta_score != 0.0:
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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45 --meta-score '$meta_score'
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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46 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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47 #if $score != 0.0:
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48 --score '$score'
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49 #end if
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50 #if $protein:
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51 '$protein'
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52 #end if
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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53 #if $min_orf_length != 90:
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54 --min-orf-length '$min_orf_length'
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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55 #end if
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56 #if $retrieve_whole:
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57 '$retrieve_whole'
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58 #end if
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59 #if $no_orf_predict:
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60 '$no_orf_predict'
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61 #end if
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62 #if $no_quality_filtering:
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63 '$no_quality_filtering'
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64 #end if
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65 #if $no_assembly:
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66 '$no_assembly'
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67 #end if
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68 #if $orf_finder:
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69 '$orf_finder'
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70 #end if
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71 #if $store_peptides:
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72 '$store_peptides'
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73 #end if
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74 &&
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75 #if $inputs.input_type in ('paired', 'collection'):
1
239ce9f24386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 0b2de0d35b6ef4c0ef0dd77e8415115a4a3b415b"
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76 tar -czf retrievedFragments.tar.gz fargene_output/retrievedFragments
0
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77 #end if
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78 2>&1
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79 ]]> </command>
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80 <inputs>
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81 <conditional name="inputs">
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82 <param name="input_type" type="select" label="Input type" help="Select 'paired end' reads or 'sequence' for genomes/contigs">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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83 <option value="paired" selected="true">Paired</option>
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84 <option value="collection">Paired Collection</option>
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85 <option value="sequence">Contigs/Genomes</option>
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86 </param>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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87 <when value="paired">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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88 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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89 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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parents:
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90 </when>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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parents:
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91 <when value="collection">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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92 <param name="input_collection" format="fastqsanger" type="data_collection" collection_type="list:paired" label="Paired collection"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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93 </when>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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94 <when value="sequence">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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95 <param name="input_sequence" type="data" format="fasta" multiple="true" label="Input contigs/genomes" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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96 </when>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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97 </conditional>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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98
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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99 <param name="models" type="select" label="Resistance Genes">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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100 <option value="class_a">Class A beta-lactamases</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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101 <option value="class_b_1_2">Subclass B1 and B2 beta-lactamases</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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102 <option value="class_b_3">Subclass B3 beta-lactamases</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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103 <option value="class_c">Class C beta-lactamases</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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104 <option value="class_d_1">Class D beta-lactamases-1</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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parents:
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105 <option value="class_d_2">Class D beta-lactamases-2</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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106 <option value="qnr">QNR</option>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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107 </param>
2
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108 <param argument="--score" type="float" value="0.0" label="The threshold score for a sequence to be classified as a (almost) complete gene" />
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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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" />
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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110 <param argument="--protein" type="boolean" truevalue="--protein" falsevalue="" checked="False" label="Rescue short unassmebled plasmids" />
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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111 <param argument="--min-orf-length" type="integer" min="1" value="90" label="The minimal length for a retrieved predicted ORF (nt)" />
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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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" />
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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113 <param argument="--no-orf-predict" type="boolean" truevalue="--no-orf-predict" falsevalue="" checked="False" label="Do not perform ORF prediction" />
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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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" />
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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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" />
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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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" />
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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117 <param argument="--store-peptides" type="boolean" truevalue="--store-peptides" falsevalue="" checked="False" label="Store the translated sequences"
b982a9ea939c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
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118 help="Useful if you plan to redo the analysis using a different model and want to skip the preprocessing steps" />
0
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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119
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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120 </inputs>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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121 <outputs>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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122 <data name="summary" format="txt" from_work_dir="fargene_output/results_summary.txt" label="${tool.name} on ${on_string} (Summary)">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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123 </data>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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124 <data name="retrievedFragments" format="tar.gz" from_work_dir="retrievedFragments.tar.gz" label="${tool.name} on ${on_string} (Retrieved Fragments)">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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125 <filter>inputs["input_type"] in ['paired' , 'collection']</filter>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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126 </data>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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127 <data name="fargene_log" format="txt" from_work_dir="fargene_analysis.log" label="${tool.name} on ${on_string} (log)">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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128 </data>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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129 <collection name="hmmsearchresults" type="list" label="HMM Search Result">
1
239ce9f24386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 0b2de0d35b6ef4c0ef0dd77e8415115a4a3b415b"
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parents: 0
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130 <discover_datasets pattern="(?P&lt;name&gt;.+).out" directory="fargene_output/hmmsearchresults" format="txt" visible="false" />
0
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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131 </collection>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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132 <collection name="predictedGenes" type="list" label="Predicted Genes">
1
239ce9f24386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 0b2de0d35b6ef4c0ef0dd77e8415115a4a3b415b"
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parents: 0
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133 <discover_datasets pattern="(?P&lt;name&gt;.+).fasta" directory="fargene_output/predictedGenes" format="fasta" visible="false" />
0
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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134 </collection>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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135 </outputs>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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136 <tests>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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137 <test expect_num_outputs="5">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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138 <conditional name="inputs">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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139 <param name="input_type" value="paired"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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140 <param name="R1" value="reads_1.fastq"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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141 <param name="R2" value="reads_2.fastq"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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142 </conditional>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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143 <output name="summary" file="paired/results_summary.txt" compare="sim_size"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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144 </test>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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145 <test expect_num_outputs="5">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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146 <conditional name="inputs">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
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147 <param name="input_type" value="collection"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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148 <param name="input_collection">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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149 <collection type="list:paired">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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150 <element name="Pair1">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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151 <collection type="paired">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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152 <element name="forward" value="reads_1.fastq" ftype="fastqsanger"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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153 <element name="reverse" value="reads_2.fastq" ftype="fastqsanger"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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154 </collection>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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155 </element>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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156 </collection>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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157 </param>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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158 </conditional>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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159 <output name="summary" file="paired/results_summary.txt" compare="sim_size"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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160 </test>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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161 <test expect_num_outputs="4">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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162 <conditional name="inputs">
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
iuc
parents:
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163 <param name="input_type" value="sequence"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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164 <param name="input_sequence" value="klebsiella_plasmid.fasta"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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165 <param name="models" value="class_b_1_2" />
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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166 </conditional>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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167 <output name="summary" file="contigs/results_summary.txt" compare="sim_size"/>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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168 </test>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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169 </tests>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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170 <help><![CDATA[
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171
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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172 fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. The tool includes developed and optimized models for a number or resistance gene types, and the functionality to create and optimize models of your own choice of resistance genes.
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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173
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174 The current version of the tool includes developed and optimized models for identification of the following resistance genes
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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175
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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176 - Class A beta-lactamases
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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177 - Subclass B1 and B2 beta-lactamases
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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178 - Subclass B3 beta-lactamases
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179 - Class C beta-lactamases
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180 - Class D beta-lactamases
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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181 - qnr
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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182 ]]>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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183 </help>
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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184 <expand macro="citations" />
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185 </tool>