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74
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1 <tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="@WRAPPER_VERSION@.3.0">
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28
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2 <description>post-processes de novo transcriptome assembly</description>
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37
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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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74
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6 <requirements>
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7 <requirement type="package" version="1.0.3">plant_tribes_assembly_post_processor</requirement>
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8 </requirements>
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70
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9 <command detect_errors="exit_code"><![CDATA[
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10 python '$__tool_directory__/assembly_post_processor.py'
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70
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11 --transcripts '$input'
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12 --prediction_method $prediction_method_cond.prediction_method
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13 #if str($prediction_method_cond.prediction_method) == 'estscan':
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14 --score_matrices '$score_matrices'
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15 #end if
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16 #if str($options_type.options_type_selector) == 'advanced':
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17 #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond
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18 #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
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19 --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
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20 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
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21 --method '$target_gene_family_assembly_cond.method'
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22 --gap_trimming $target_gene_family_assembly_cond.gap_trimming
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23 #end if
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24 #if str($options_type.strand_specific) == 'yes':
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72
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25 --strand_specific true
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70
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26 #end if
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27 #if str($options_type.dereplicate) == 'yes':
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72
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28 --dereplicate true
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29 --output_cleaned_nr_cds '$output_cleaned_nr_cds'
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30 --output_cleaned_nr_pep '$output_cleaned_nr_pep'
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31 #end if
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32 --min_length $options_type.min_length
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33 #end if
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34 --num_threads \${GALAXY_SLOTS:-4}
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35 --output_cds '$output_cds'
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36 --output_cleaned_cds '$output_cleaned_cds'
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37 --output_cleaned_pep '$output_cleaned_pep'
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38 --output_pep '$output_pep'
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39 ]]></command>
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0
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40 <inputs>
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28
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41 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
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0
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42 <conditional name="prediction_method_cond">
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28
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43 <param name="prediction_method" type="select" label="Coding regions prediction method">
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0
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44 <option value="transdecoder" selected="true">TransDecoder</option>
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45 <option value="estscan">ESTScan</option>
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46 </param>
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47 <when value="transdecoder" />
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48 <when value="estscan">
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49 <param name="score_matrices" format="smat" type="data" label="Scores matrices"/>
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50 </when>
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51 </conditional>
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52 <conditional name="options_type">
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53 <param name="options_type_selector" type="select" label="Options configuration">
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0
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54 <option value="basic" selected="true">Basic</option>
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55 <option value="advanced">Advanced</option>
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56 </param>
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57 <when value="basic" />
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58 <when value="advanced">
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59 <conditional name="target_gene_family_assembly_cond">
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28
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60 <param name="target_gene_family_assembly" type="select" label="Perform targeted gene assembly?">
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0
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61 <option value="no" selected="true">No</option>
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62 <option value="yes">Yes</option>
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63 </param>
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64 <when value="no" />
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65 <when value="yes">
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28
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66 <param name="orthogroups" format="tabular" type="data" label="Targeted gene families"/>
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33
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67 <param name="scaffold" type="select" label="Gene family scaffold">
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0
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68 <options from_data_table="plant_tribes_scaffolds" />
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10
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69 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
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0
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70 </param>
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71 <param name="method" type="select" label="Protein clustering method">
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72 <option value="gfam" selected="true">GFam</option>
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73 <option value="orthofinder">OrthoFinder</option>
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74 <option value="orthomcl">OrthoMCL</option>
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75 </param>
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39
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76 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Trim alignments"/>
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0
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77 </when>
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78 </conditional>
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28
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79 <param name="strand_specific" type="select" label="Strand-specific assembly?">
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0
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80 <option value="no" selected="true">No</option>
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81 <option value="yes">Yes</option>
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82 </param>
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28
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83 <param name="dereplicate" type="select" label="Remove duplicate sequences?">
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0
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84 <option value="no" selected="true">No</option>
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85 <option value="yes">Yes</option>
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86 </param>
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28
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87 <param name="min_length" type="integer" value="200" label="Minimum sequence length"/>
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0
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88 </when>
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89 </conditional>
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90 </inputs>
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91 <outputs>
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80
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92 <collection name="output_targeted_gene_families" type="list" label="Targeted gene families: ${tool.name} on ${on_string}">
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82
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93 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir/targeted_gene_family_assemblies" format="fasta" />
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62
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94 <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter>
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80
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95 </collection>
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68
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96 <data name="output_pep" format="fasta" label="transcripts.pep: ${tool.name} on ${on_string}"/>
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97 <data name="output_cleaned_pep" format="fasta" label="transcripts.cleaned.pep: ${tool.name} on ${on_string}"/>
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98 <data name="output_cleaned_nr_pep" format="fasta" label="transcripts.cleaned.nr.pep: ${tool.name} on ${on_string}">
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66
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99 <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter>
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100 </data>
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68
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101 <data name="output_cleaned_nr_cds" format="fasta" label="transcripts.cleaned.nr.cds: ${tool.name} on ${on_string}">
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66
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102 <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter>
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103 </data>
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68
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104 <data name="output_cleaned_cds" format="fasta" label="transcripts.cleaned.cds: ${tool.name} on ${on_string}"/>
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105 <data name="output_cds" format="fasta" label="transcripts.cds: ${tool.name} on ${on_string}"/>
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0
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106 </outputs>
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107 <tests>
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108 <test>
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66
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109 <param name="input" value="assembly.fasta" ftype="fasta"/>
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110 <param name="prediction_method" value="transdecoder"/>
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111 <output name="output_cds" file="transcripts.cds" ftype="fasta"/>
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112 <output name="output_cleaned_cds" file="transcripts.cleaned.cds" ftype="fasta"/>
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69
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113 <output name="output_cleaned_pep" file="transcripts.cleaned.pep" ftype="fasta"/>
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66
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114 <output name="output_pep" file="transcripts.pep" ftype="fasta"/>
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6
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115 </test>
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116 <test>
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66
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117 <param name="input" value="assembly.fasta" ftype="fasta"/>
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118 <param name="prediction_method" value="estscan"/>
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55
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119 <param name="score_matrices" value="arabidopsis_thaliana.smat" ftype="smat"/>
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66
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120 <param name="options_type_selector" value="advanced"/>
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121 <param name="dereplicate" value="yes"/>
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122 <output name="output_cds" file="transcripts2.cds" ftype="fasta"/>
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123 <output name="output_cleaned_cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
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124 <output name="output_cleaned_nr_cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
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125 <output name="output_cleaned_nr_pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
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126 <output name="output_cleaned_pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
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127 <output name="output_pep" file="transcripts2.pep" ftype="fasta"/>
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128 </test>
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129 <test>
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130 <param name="input" value="assembly_tgf.fasta" ftype="fasta"/>
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131 <param name="prediction_method" value="transdecoder"/>
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132 <param name="options_type_selector" value="advanced"/>
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133 <param name="target_gene_family_assembly" value="yes"/>
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134 <param name="orthogroups" value="target_orthos.ids"/>
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135 <param name="scaffold" value="22Gv1.1"/>
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136 <param name="method" value="orthomcl"/>
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137 <param name="dereplicate" value="yes"/>
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82
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138 <output_collection name="output_targeted_gene_families" type="list">
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139 <element name="752.faa" file="752.faa" ftype="fasta"/>
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140 <element name="752.fasta" file="752.fasta" ftype="fasta"/>
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141 <element name="752.fna" file="752.fna" ftype="fasta"/>
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142 </output_collection>
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66
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143 <output name="output_cds" file="transcripts_tgf.cds" ftype="fasta"/>
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144 <output name="output_cleaned_cds" file="transcripts.cleaned_tgf.cds" ftype="fasta"/>
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145 <output name="output_cleaned_nr_cds" file="transcripts_tgf.cleaned.nr.cds" ftype="fasta"/>
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146 <output name="output_cleaned_nr_pep" file="transcripts_tgf.cleaned.nr.pep" ftype="fasta"/>
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147 <output name="output_cleaned_pep" file="transcripts.cleaned_tgf.pep" ftype="fasta"/>
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148 <output name="output_pep" file="transcripts_tgf.pep" ftype="fasta"/>
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0
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149 </test>
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150 </tests>
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151 <help>
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33
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152 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and
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28
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153 evolutionary analyses of genome-scale gene families and transcriptomes. This tool post-processes de novo
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154 assembled transcripts into putative coding sequences and their corresponding amino acid translations and
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155 optionally assigns transcripts to circumscribed gene families ("orthogroups")[2]. After transcripts have been
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156 assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the
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157 de novo assembly.
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0
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158
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159 -----
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160
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28
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161 **Required options**
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162
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163 * **Transcriptome assembly fasta file** - either de novo or reference-guided transcriptome assembly fasta file selected from your history.
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33
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164 * **Coding regions prediction method** - method for finding coding regions within transcripts. Available methods are TransDecoder[3] and ESTScan[4].
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165 * **Scores matrices** - scores matrices, based on a related species, are required when ESTScan is used to find coding regions. Details of how to create species-specific scores matrices can be found on the ESTScan website (http://estscan.sourceforge.net). Matrices of some organisms are also available to download.
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28
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166
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167 **Other options**
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0
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168
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29
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169 * **Perform targeted gene assembly?** - selecting 'Yes' enables local assembly of one or more targeted gene families in a specific scaffold. Scaffolds are defined in PlantTribes as clusters of paralogous/orthologous sequences from a specified set of proteomes[5-7].
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35
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170
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39
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171 * **Targeted gene families** - select a history item containing a list of targeted orthogroup identifiers corresponding to the gene family classification from a specified scaffold. Gene family identifiers can be obtained from the function annotation table ("Orthogroup ID" field of .summary file) of scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and also available at the PlantTribes github repository (https://github.com/dePamphilis/PlantTribes/tree/master/config).
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35
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172 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds (installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool) whose orthogroup(s) are targeted for the localized assembly.
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173 * **Protein clustering method** - gene family scaffold protein clustering method. Each PlantTribes scaffold data has up to three sets of clusters - GFam[8] (clusters of consensus domain architecture), OrthoFinder[9] (broadly defined clusters) or OrthoMCL[10] (narrowly defined clusters). You can also install your own data scaffold created using a different clustering method as long as it conforms to the PlantTribes scaffold data format.
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39
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174 * **Trim alignments** - trim gene family multiple sequence alignments that include scaffold backbone genes and locally assembled transcripts to remove non-conserved regions (gappy sites)[11]. The trimmed alignments are used in assigning scores to locally assembled transcripts to determine how well they compare to the backbone gene models. The default setting of 0.1 removes sites that have gaps in 90% or more of the sequences in the multiple sequence alignment. This option is restricted to the range 0.0 - 1.0.
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35
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175
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28
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176 * **Strand-specific assembly?** - select 'Yes' if transcriptome library sequences were strand-specific. If 'Yes" is selected, transcripts from the minority strand (antisense) are removed.
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177 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
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178 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp.
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31
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179
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0
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180 </help>
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181 <citations>
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37
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182 <expand macro="citation1" />
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28
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183 <citation type="bibtex">
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29
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184 @article{Honaas2016,
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185 journal = {PloS one},
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186 author = {2. Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH},
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28
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187 title = {Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome},
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188 year = {2016},
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189 volume = {11},
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190 number = {1},
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29
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191 pages = {e0146062},}
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28
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192 </citation>
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24
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193 <citation type="bibtex">
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29
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194 @article{Haas2013,
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195 journal = {Nature Protocols},
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196 author = {3. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD},
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28
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197 title = {De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis},
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198 year = {2013},
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199 volume = {8},
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200 number = {8},
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29
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201 pages = {1494-1512},}
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28
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202 </citation>
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203 <citation type="bibtex">
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29
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204 @article{Iseli1999,
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205 journal = {ISMB},
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206 author = {4. Iseli C, Jongeneel CV, Bucher P},
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207 title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences},
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24
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208 year = {1999},
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28
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209 volume = {99},
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29
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210 pages = {138-148},
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211 url = {http://estscan.sourceforge.net},}
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28
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212 </citation>
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213 <citation type="bibtex">
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29
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214 @article{Huang1999,
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215 journal = {Genome Research},
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216 author = {5. Huang X, Madan A},
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28
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217 title = {CAP3: A DNA sequence assembly program},
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218 year = {1999},
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219 volume = {9},
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220 number = {9},
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29
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221 pages = {868-877},
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222 url = {http://seq.cs.iastate.edu/cap3.html},}
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28
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223 </citation>
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224 <citation type="bibtex">
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29
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225 @article{Eddy2009,
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226 journal = {Genome Inform},
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227 author = {6. Eddy SR},
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28
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228 title = {A new generation of homology search tools based on probabilistic inference},
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229 year = {2009},
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230 volume = {23},
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231 number = {1},
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29
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232 pages = {205-211},}
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28
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233 </citation>
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234 <citation type="bibtex">
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30
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235 @article{Katoh2013,
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236 journal = {Molecular biology and evolution},
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237 author = {7. Katoh K, Standley DM},
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238 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
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239 year = {2013},
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240 volume = {30},
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241 number = {4},
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242 pages = {772-780},}
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243 </citation>
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244 <citation type="bibtex">
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29
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245 @article{Sasidharan2012,
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246 journal = {Nucleic Acids Research},
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30
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247 author = {8. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
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28
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248 title = {GFam: a platform for automatic annotation of gene families},
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249 year = {2012},
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29
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250 pages = {gks631},}
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28
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251 </citation>
|
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252 <citation type="bibtex">
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29
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253 @article{Li2003,
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254 journal = {Genome Research}
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30
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255 author = {9. Li L, Stoeckert CJ, Roos DS},
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28
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256 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
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257 year = {2003},
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258 volume = {13},
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259 number = {9},
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29
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260 pages = {2178-2189},}
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28
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261 </citation>
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262 <citation type="bibtex">
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29
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263 @article{Emms2015,
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264 journal = {Genome Biology}
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30
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265 author = {10. Emms DM, Kelly S},
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28
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266 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
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267 year = {2015},
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268 volume = {16},
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269 number = {1},
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29
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270 pages = {157},}
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28
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271 </citation>
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272 <citation type="bibtex">
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29
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273 @article{Capella-Gutierrez2009,
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274 journal = {Bioinformatics,},
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30
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275 author = {11. Capella-Gutierrez S, Silla-MartÃnez JM, Gabaldón T},
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28
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276 title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
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277 year = {2009},
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278 volume = {25},
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279 number = {15},
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29
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280 pages = {1972-1973},}
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28
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281 </citation>
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282 <citation type="bibtex">
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29
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283 @article{Gremme2013,
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284 journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
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30
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285 author = {12. Gremme G, Steinbiss S, Kurtz S},
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28
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286 title = {GenomeTools: a comprehensive software library for efficient processing of structured genome annotations},
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287 year = {2013},
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288 volume = {10},
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289 number = {3},
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29
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290 pages = {645-656},}
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28
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291 </citation>
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0
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292 </citations>
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293 </tool>
|
