Mercurial > repos > iuc > chewbbaca_createschema

annotate CreateSchema.xml @ 0:1fc5ac7a8dce 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 14:13:09 +0000
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0
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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1 <tool id="chewbbaca_createschema" name="chewBBACA CreateSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Create a gene-by-gene schema</description>
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3 <macros>
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iuc
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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' &&
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10 #for $file in $input_file
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11 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($file.element_identifier))
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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12 ln -sf '$file' 'input/${escaped_element_identifier}.${file.ext}' &&
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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13 #end for
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14 chewBBACA.py CreateSchema
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15 #if $training_file:
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16 --ptf '$training_file'
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17 #end if
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18 $cds_input
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19 @COMMON_INPUT@
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20 --pm $prodigal_mode
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21 -i 'input' -o 'output' &&
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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22 cd 'output/' &&
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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23 zip -r schema_seed.zip 'schema_seed'
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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24 ]]></command>
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25 <inputs>
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26 <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/>
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27 <section name="advanced" title="Advanced options">
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28 <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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29 <param argument="--cds-input" type="boolean" truevalue="--cds-input" falsevalue="" checked="false" label="CDS input" optional="true"/>
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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30 <param argument="--minimum-length" type="integer" min="0" value="201" label="Minimum sequence length value"/>
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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31 <expand macro="common_param" />
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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32 <param argument="--prodigal-mode" type="select" 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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33 <option value="single" selected="true">
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34 single
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35 </option>
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36 <option value="meta">
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37 meta
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38 </option>
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39 </param>
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40 </section>
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41 <section name="output" title="Output options">
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42 <param name="show_cds_invalid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output invalid CDS file?"/>
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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43 <param name="show_cds_coord" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output CDS coordinates File?"/>
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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44 </section>
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45 </inputs>
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46 <outputs>
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47 <data format="zip" name="schema" from_work_dir="output/schema_seed.zip" label="${tool.name} on ${on_string}: Schema files"/>
1fc5ac7a8dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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48 <data format="txt" name="txt_file" from_work_dir="output/invalid_cds.txt" label="${tool.name} on ${on_string}: Invalid CDS">
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49 <filter>output['show_cds_invalid']</filter>
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50 </data>
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51 <data format="tabular" name="tsv_file" from_work_dir="output/cds_coordinates.tsv" label="${tool.name} on ${on_string}: CDS coordinates">
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52 <filter>output['show_cds_coord']</filter>
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53 </data>
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54 </outputs>
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55 <tests>
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56 <test expect_num_outputs="1">
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57 <param name="input_file" value="GCA_000007265.fna"/>
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58 <output name="schema">
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59 <assert_contents>
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60 <has_archive_member path="schema_seed/.*\.fasta" n="204"/>
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61 <has_archive_member path="schema_seed/short/.*\.fasta" n="102"/>
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62 <has_archive_member path="schema_seed/\.schema_config"/>
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63 </assert_contents>
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64 </output>
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65 </test>
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66 <test expect_num_outputs="1">
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67 <param name="input_file" value="GCA_000007265"/>
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68 <output name="schema">
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69 <assert_contents>
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70 <has_archive_member path="schema_seed/.*\.fasta" n="204"/>
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71 <has_archive_member path="schema_seed/short/.*\.fasta" n="102"/>
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72 <has_archive_member path="schema_seed/\.schema_config"/>
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73 </assert_contents>
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74 </output>
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75 </test>
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76 <test expect_num_outputs="1">
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77 <param name="input_file" value="GCA_000007265.fna"/>
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78 <param name="training_file" value="Streptococcus_agalactiae.trn"/>
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79 <output name="schema">
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80 <assert_contents>
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81 <has_archive_member path="schema_seed/.*\.fasta" n="198"/>
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82 <has_archive_member path="schema_seed/short/.*\.fasta" n="99"/>
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83 <has_archive_member path="schema_seed/\.schema_config"/>
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84 </assert_contents>
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85 </output>
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86 </test>
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87 <test expect_num_outputs="1">
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88 <param name="input_file" value="CDS_Str_agalactiae.fasta"/>
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89 <param name="cds_input" value="true"/>
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90 <output name="schema">
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91 <assert_contents>
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92 <has_archive_member path="schema_seed/CDS-Str-agalactiae-fasta-protein1.fasta"/>
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93 </assert_contents>
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94 </output>
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95 </test>
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96 </tests>
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97 <help>
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98
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99 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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100
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101 A Schema is a pre-defined set of loci that is used in MLST analyses. Traditional MLST schemas relied in 7 loci that were internal fragments of housekeeping genes and each locus was defined by its amplification by a pair of primers yielding a fragment of a defined size.
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102
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103 In genomic analyses, schemas are a set of loci that are:
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104
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105 - Present in the majority of strains for core genome (cg) MLST schemas, typically a threshold of presence in 95% of the strains is used in schema creation. The assumption is that in each strain up to 5% of loci may not be identified due to sequencing coverage problems, assembly problems or other issues related to the use of draft genome assemblies.
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106 - Present in at least one of the analyzed strains in the schema creation for pan genome/whole genome (pg/wg) MLST schemas.
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107 - Present in less than 95% of the strains for accessory genome (ag) MLST schemas.
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108
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109 .. class:: infomark
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110
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111 **Note**
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112
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113 These definitions are always operational in nature, in the sense that the analyses are performed on a limited number of strains representing part of the biological diversity of a given species or genus and are always dependent on the definition of thresholds.
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114
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115 .. class:: infomark
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116
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117 **Important**
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118
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119 The use of a prodigal training file for schema creation is highly recommended.
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120
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121 .. class:: infomark
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122
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123 **Important**
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124
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125 If you provide the **--cds-input** parameter, chewBBACA assumes that the input FASTA files contain coding sequences and skips the gene prediction step with Prodigal. To avoid issues related with the format of the sequence headers, chewBBACA renames the sequence headers based on the unique basename prefix determined for each input file and on the order of the coding sequences (e.g.: coding sequences inside a file named GCF_000007125.1_ASM712v1_cds_from_genomic.fna are renamed to GCF_000007125-protein1, GCF_000007125-protein2, …, GCF_000007125-proteinN).
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126
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127 </help>
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128 <expand macro="citations" />
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129 </tool>