Mercurial > repos > iuc > chewbbaca_allelecall

annotate AlleleCall.xml @ 0:1ac58e449c87 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
author iuc
date Wed, 25 Sep 2024 14:12:27 +0000
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0
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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1 <tool id="chewbbaca_allelecall" name="ChewBBACA AlleleCall" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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2 <description>Determine the allelic profiles of a set of genomes</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import re
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9 mkdir 'input' &&
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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10 mkdir 'schema' &&
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11 #for $file in $input_file
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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12 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($file.element_identifier))
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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13 ln -sf '$file' 'input/${escaped_element_identifier}.${file.ext}' &&
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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14 #end for
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15 unzip '$input_schema' -d 'schema' &&
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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16 chewBBACA.py AlleleCall
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17 #if $training_file:
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18 --ptf '$training_file'
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19 #end if
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20 $cds_input
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21 #if $genes_list:
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22 --gl '$genes_list'
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23 #end if
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24 #if str($blast_score_ratio) != ""
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25 --bsr $blast_score_ratio
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26 #end if
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27 #if str($minimum_length) != ""
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28 --l $minimum_length
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29 #end if
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30 #if str($translation_table) != ""
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31 --t $translation_table
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32 #end if
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33 #if str($size_threshold) != ""
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34 --st $size_threshold
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35 #end if
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36 $no_inferred
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37 --pm $prodigal_mode
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38 --mode $mode
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39 --force-continue
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40 #if 'output_unclassified' in $output_selector:
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41 --output-unclassified
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42 #end if
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43 #if 'output_missing' in $output_selector:
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44 --output-missing
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45 #end if
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46 #if 'output_novel' in $output_selector:
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47 --output-novel
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48 #end if
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49 #if 'hash_profile' in $output_selector:
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50 ## It can use any hashing algorithm from hashlib but for simplicity we set it to md5
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51 --hash-profile md5
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52 #end if
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53 -i 'input' -g 'schema/schema_seed/' -o 'output'
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54 ]]></command>
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55 <inputs>
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56 <param format="fasta" name="input_file" type="data" multiple="true" label="Genome assemblies in FASTA format"/>
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57 <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
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58 <section name="advanced" title="Advanced options">
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59 <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" />
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60 <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" help="By default, gets the training file from the schema"/>
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61 <param argument="--cds-input" type="boolean" truevalue="--cds-input" falsevalue="" checked="false" label="CDS input" optional="true"/>
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62 <param argument="--blast-score-ratio" type="float" min="0.0" max="1.0" value="" optional="true" label="BLAST Score Ratio value" />
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63 <param argument="--minimum-length" type="integer" min="0" value="" optional="true" label="Minimum sequence length value"/>
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64 <param argument="--translation-table" type="integer" min="0" value="" optional="true" help="Must match the genetic code used to create the training file (default: uses value defined in schema config)." label="Genetic code used to predict genes and to translate coding sequences"/>
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65 <param argument="--size-threshold" type="float" min="0" value="" optional="true" label="CDS size variation threshold"/>
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66 <param argument="--no-inferred" type="boolean" truevalue="--no-inferred" falsevalue="" checked="false" optional="true" label="Add the sequences of inferred alleles (INF) to the schema" help="Use this parameter if the schema is being accessed by multiple processes/users simultaneously." />
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67 <param argument="--prodigal-mode" type="select" optional="true" label="Prodigal Mode" help="&quot;single&quot; for finished genomes, reasonable quality draft genomes and big viruses. &quot;meta&quot; for metagenomes, low quality draft genomes, small viruses, and small plasmids">
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68 <option value="single" selected="true">
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69 single
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70 </option>
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71 <option value="meta">
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72 meta
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73 </option>
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74 </param>
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75 <param argument="--mode" type="select" label="Execution mode" optional="true">
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76 <option value="1">Only exact matches at DNA level</option>
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77 <option value="2">Exact matches at DNA and Protein level </option>
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78 <option value="3">Exact matches and minimizer-based clustering to find similar alleles based on BSR+0.1 </option>
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79 <option value="4" selected="true">Exact matches and minimizer-based clustering to find similar alleles based on BSR+0.1 </option>
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80 </param>
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81 </section>
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82 <section name="output" title="Output Options">
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83 <param name="output_selector" type="select" multiple="true" optional="true" display="checkboxes" label="Select / Deselect all">
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84 <option value="output_unclassified">Create a Fasta file with unclassified coding sequences. (--output-unclassified)</option>
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85 <option value="output_missing">Create a Fasta file with coding sequences classified as NIPH, NIPHEM, ASM, ALM, PLOT3, PLOT5 and LOTSC. (--output-missing)</option>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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86 <option value="output_novel">Create Fasta file with the novel alleles inferred during the allele calling. (--output-novel)</option>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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87 <option value="hash_profile">Create TSV file with hashed allelic profiles. (--hash-profile) </option>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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88 </param>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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89 </section>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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90 </inputs>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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91 <outputs>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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92 <collection name="allelecall_results" type="list" label="${tool.name} on ${on_string}: AlleleCall Results">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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93 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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94 </collection>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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95 <collection name="allelcall_log" type="list" label="${tool.name} on ${on_string}: AlleleCall Logs">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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96 <discover_datasets pattern="(?P&lt;name&gt;.+)\.txt$" format="txt" directory="output"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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97 </collection>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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98 <data name="unclassified_fasta" format="fasta" from_work_dir="output/unclassified_sequences.fasta" label="${tool.name} on ${on_string}: Unclassified fasta">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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99 <filter>output['output_selector'] and 'output_unclassified' in output['output_selector']</filter>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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100 </data>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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101 <data name="missing_fasta" format="fasta" from_work_dir="output/missing_classes.fasta" label="${tool.name} on ${on_string}: Missing fasta">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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102 <filter>output['output_selector'] and 'output_missing' in output['output_selector']</filter>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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103 </data>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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104 <data name="novel_fasta" format="fasta" from_work_dir="output/novel_alleles.fasta" label="${tool.name} on ${on_string}: Novel fasta">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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105 <filter>output['output_selector'] and 'output_novel' in output['output_selector']</filter>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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106 </data>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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107 </outputs>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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108 <tests>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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109 <test expect_num_outputs="4">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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110 <param name="input_file" value="GCA_000007265"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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111 <param name="input_schema" value="schema.zip"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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112 <param name="output_selector" value="output_unclassified,output_missing,hash_profile" />
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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113 <output_collection name="allelecall_results" type="list">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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114 <element name="cds_coordinates" file="cds_coordinates.tsv" compare="diff"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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115 <element name="loci_summary_stats" file="loci_summary_stats.tsv" compare="diff"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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116 <element name="paralogous_loci" ftype="tabular">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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117 <assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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118 <has_text_matching expression="Genome.*Loci.*CDS"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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119 </assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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120 </element>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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121 <element name="results_alleles" ftype="tabular">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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122 <assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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123 <has_text_matching expression="1.*1.*NIPHEM.*1.*1"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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124 <has_text_matching expression="GCA_000007265.*1"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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125 </assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
126 </element>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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127 <element name="results_alleles" file="results_alleles.tsv" compare="diff"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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128 <element name="results_alleles_hashed" ftype="tabular">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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129 <assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
130 <has_text_matching expression="FILE.*GCA-000007265-protein1.*GCA-000007265-protein10.*GCA-000007265-protein100"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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131 <has_text_matching expression="GCA_000007265.*308e7666834338d0530d925b2737f2c6.*4aece26d201d59a90947e3400c7abf3f.*ebea148832aa2ae2704d37ebd5123169"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
132 </assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
133 </element>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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134 <element name="results_statistics" file="results_statistics.tsv" compare="diff"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
135 </output_collection>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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136 <output_collection name="allelcall_log" type="list">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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137 <element name="logging_info" ftype="txt">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
138 <assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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139 <has_text_matching expression="Used a BSR of: 0.6"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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140 </assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
141 </element>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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142 </output_collection>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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143 <output name="unclassified_fasta">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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144 <assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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145 <has_text_matching expression="GCA_000007265-protein15"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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146 <has_text_matching expression="ATGCACCACCTGTCACTTCTGCTCCGAAGAGAAAGCCTATCTCTAGGCCGGTCAGAAGGATGTCAAGACCTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAG"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
147 </assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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148 </output>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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149 <output name="missing_fasta">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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150 <assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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151 <has_text_matching expression="1|GCA_000007265|GCA-000007265-protein16&amp;NIPHEM|GCA_000007265-protein16&amp;EXC"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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152 </assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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153 </output>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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154 </test>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
155 <test expect_num_outputs="4">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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156 <param name="input_file" value="GCA_000007265.fna"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
157 <param name="input_schema" value="schema.zip"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
158 <param name="output_selector" value="output_unclassified,output_missing,hash_profile" />
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
159 <output_collection name="allelecall_results" type="list">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
160 <element name="paralogous_loci" ftype="tabular">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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diff changeset
161 <assert_contents>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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162 <has_text_matching expression="Genome.*Loci.*CDS"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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163 </assert_contents>
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iuc
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diff changeset
164 </element>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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165 <element name="results_alleles" ftype="tabular">
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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166 <assert_contents>
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iuc
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diff changeset
167 <has_text_matching expression="1.*1.*NIPHEM.*1.*1"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
iuc
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168 <has_text_matching expression="GCA_000007265.*1"/>
1ac58e449c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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169 </assert_contents>
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170 </element>
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171 <element name="results_alleles_hashed" ftype="tabular">
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172 <assert_contents>
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173 <has_text_matching expression="FILE.*GCA-000007265-protein1.*GCA-000007265-protein10.*GCA-000007265-protein100"/>
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174 <has_text_matching expression="GCA_000007265_fna.*308e7666834338d0530d925b2737f2c6.*4aece26d201d59a90947e3400c7abf3f.*ebea148832aa2ae2704d37ebd5123169"/>
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175 </assert_contents>
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176 </element>
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177 </output_collection>
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178 <output_collection name="allelcall_log" type="list">
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179 <element name="logging_info" ftype="txt">
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180 <assert_contents>
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181 <has_text_matching expression="Used a BSR of: 0.6"/>
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182 </assert_contents>
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183 </element>
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184 </output_collection>
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185 <output name="unclassified_fasta">
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186 <assert_contents>
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187 <has_text_matching expression="GCA_000007265_fna-protein83"/>
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188 <has_text_matching expression="ATGCACCACCTGTCACTTCTGCTCCGAAGAGAAAGCCTATCTCTAGGCCGGTCAGAAGGATGTCAAGACCTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAG"/>
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189 </assert_contents>
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190 </output>
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191 <output name="missing_fasta">
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192 <assert_contents>
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193 <has_text_matching expression="1|GCA_000007265|GCA-000007265-protein16&amp;NIPHEM|GCA_000007265-protein16&amp;EXC"/>
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194 </assert_contents>
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195 </output>
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196 </test>
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197 </tests>
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198 <help>
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199 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
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200
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201 In chewBBACA, by default, an allele needs to be a CDS defined by Prodigal_. To ensure reproducibility of the CDS prediction, the same Prodigal training file for each bacterial species should be used and provided as input.
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202
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203 .. class:: infomark
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204
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205 **Important**
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206
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207 Although the use of a training file is optional, it is highly recommended to ensure consistent results.
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208
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209 If the schema files are created by chewBBACA v2, please use the PrepExternalSchema module to convert the schema to a format fully compatible with chewBBACA v3.
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210
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211 By default, the AlleleCall module uses the Prodigal training file included in the schema’s directory and it is not necessary to pass a training file to the --ptf parameter.
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212
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213 .. class:: infomark
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214
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215 **Note**
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216
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217 If a text file that contains a list of full paths to loci FASTA files or loci IDs, one per line, is passed to the --genes-list parameter, the process will only perform allele calling for the loci in that list.
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218
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219 .. _Prodigal: https://github.com/hyattpd/Prodigal
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220 </help>
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221 <expand macro="citations" />
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222 </tool>