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1 <tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="0.4.0">
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2 <description>post-processes de novo transcriptome assembly</description>
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0
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3 <requirements>
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4 <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
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0
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5 </requirements>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <exit_code range="1:" />
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6
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9 <exit_code range=":-1" />
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10 <!-- In case the return code has not been set propery check stderr too -->
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11 <regex match="Error:" />
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12 <regex match="Exception:" />
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13 </stdio>
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14 <command>
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15 <![CDATA[
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16 AssemblyPostProcesser
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15
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17 --transcripts '$input'
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18 --prediction_method $prediction_method_cond.prediction_method
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19 #if str($prediction_method_cond.prediction_method) == 'estscan':
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20 --score_matrices '$score_matrices'
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21 #end if
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22 #if str($options_type.options_type_selector) == 'advanced':
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23 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
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24 --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
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21
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25 --scaffold '$options_type.target_gene_family_assembly_cond.scaffold.fields.path'
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26 --method '$options_type.target_gene_family_assembly_cond.method'
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27 #end if
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28 --gap_trimming $options_type.gap_trimming
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29 #if str($options_type.strand_specific) == 'yes':
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30 --strand_specific
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31 #end if
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32 #if str($options_type.dereplicate) == 'yes':
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33 --dereplicate
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34 #end if
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35 --min_length $options_type.min_length
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36 #end if
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37 --num_threads \${GALAXY_SLOTS:-4}
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25
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38 >/dev/null
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39 ]]>
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40 </command>
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41 <inputs>
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42 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
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43 <conditional name="prediction_method_cond">
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44 <param name="prediction_method" type="select" label="Coding regions prediction method">
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45 <option value="transdecoder" selected="true">TransDecoder</option>
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46 <option value="estscan">ESTScan</option>
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47 </param>
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48 <when value="transdecoder" />
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49 <when value="estscan">
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50 <param name="score_matrices" format="smat" type="data" label="Scores matrices"/>
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51 </when>
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52 </conditional>
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53 <conditional name="options_type">
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54 <param name="options_type_selector" type="select" label="Options configuration">
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55 <option value="basic" selected="true">Basic</option>
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56 <option value="advanced">Advanced</option>
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57 </param>
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58 <when value="basic" />
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59 <when value="advanced">
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60 <conditional name="target_gene_family_assembly_cond">
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28
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61 <param name="target_gene_family_assembly" type="select" label="Perform targeted gene assembly?">
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62 <option value="no" selected="true">No</option>
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63 <option value="yes">Yes</option>
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64 </param>
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65 <when value="no" />
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66 <when value="yes">
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67 <param name="orthogroups" format="tabular" type="data" label="Targeted gene families"/>
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0
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68 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
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69 <options from_data_table="plant_tribes_scaffolds" />
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70 <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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71 </param>
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72 <param name="method" type="select" label="Protein clustering method">
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73 <option value="gfam" selected="true">GFam</option>
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74 <option value="orthofinder">OrthoFinder</option>
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75 <option value="orthomcl">OrthoMCL</option>
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76 </param>
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77 </when>
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78 </conditional>
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79 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Trim alignments"/>
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80 <param name="strand_specific" type="select" label="Strand-specific assembly?">
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0
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81 <option value="no" selected="true">No</option>
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82 <option value="yes">Yes</option>
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83 </param>
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84 <param name="dereplicate" type="select" label="Remove duplicate sequences?">
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0
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85 <option value="no" selected="true">No</option>
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86 <option value="yes">Yes</option>
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87 </param>
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88 <param name="min_length" type="integer" value="200" label="Minimum sequence length"/>
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0
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89 </when>
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90 </conditional>
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91 </inputs>
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92 <outputs>
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93 <collection name="transcripts" type="list">
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1
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94 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir" visible="true" ext="fasta" />
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0
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95 </collection>
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96 </outputs>
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97 <tests>
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98 <test>
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99 <param name="input" value="assembly.fasta" ftype="fasta" />
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100 <param name="prediction_method" value="transdecoder" />
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6
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101 <output_collection name="transcripts" type="list">
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102 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
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103 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
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16
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104 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/>
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105 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
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6
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106 </output_collection>
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107 </test>
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108 <test>
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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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0
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111 <param name="options_type_selector" value="advanced" />
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7
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112 <param name="gap_trimming" value="0.1" />
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0
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113 <param name="dereplicate" value="yes" />
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7
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114 <param name="min_length" value="200" />
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0
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115 <output_collection name="transcripts" type="list">
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116 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
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117 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
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118 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
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119 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
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120 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/>
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121 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
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0
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122 </output_collection>
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123 </test>
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124 </tests>
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125 <help>
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126 This tool is one of the PlantTribes' collection of automated modular analysis pipelines for comparative and
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127 evolutionary analyses of genome-scale gene families and transcriptomes. This tool post-processes de novo
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128 assembled transcripts into putative coding sequences and their corresponding amino acid translations and
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129 optionally assigns transcripts to circumscribed gene families ("orthogroups")[2]. After transcripts have been
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130 assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the
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131 de novo assembly.
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132
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133 -----
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134
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135 **Required options**
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136
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137 * **Transcriptome assembly fasta file** - either de novo or reference-guided transcriptome assembly fasta file selected from your history.
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138 * **Coding regions prediction method** - method for finding coding recions within transcripts. Available methods are TransDecoder[3] and ESTScan[4].
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29
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139 * **Scores matrices** - scores matrices, based on a related species, are required when ESTScan is ued 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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140
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141 **Other options**
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142
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143 * **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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144 * **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 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.
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145 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds (installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool) whose orthogroups(s) are targeted for the localized assembly.
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146 * **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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147 * **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 backbones gene models. The default setting of 0.1 removes sites tha thave gaps in 90% of the sequences in the multiple sequence alignment. This option is restricted to the range 0.0 - 1.0.
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148 * **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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149 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
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150 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp.
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151
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152 </help>
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153 <citations>
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24
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154 <citation type="bibtex">
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29
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155 @article{None,
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156 journal = {None},
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157 author = {1. Wafula EK},
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28
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158 title = {Manuscript in preparation},
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24
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159 year = {None},
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29
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160 url = {https://github.com/dePamphilis/PlantTribes},}
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28
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161 </citation>
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162 <citation type="bibtex">
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29
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163 @article{Honaas2016,
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164 journal = {PloS one},
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165 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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166 title = {Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome},
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167 year = {2016},
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168 volume = {11},
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169 number = {1},
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29
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170 pages = {e0146062},}
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28
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171 </citation>
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24
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172 <citation type="bibtex">
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29
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173 @article{Haas2013,
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174 journal = {Nature Protocols},
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175 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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176 title = {De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis},
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177 year = {2013},
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178 volume = {8},
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179 number = {8},
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29
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180 pages = {1494-1512},}
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28
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181 </citation>
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182 <citation type="bibtex">
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29
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183 @article{Iseli1999,
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184 journal = {ISMB},
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185 author = {4. Iseli C, Jongeneel CV, Bucher P},
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186 title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences},
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24
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187 year = {1999},
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28
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188 volume = {99},
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29
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189 pages = {138-148},
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190 url = {http://estscan.sourceforge.net},}
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28
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191 </citation>
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192 <citation type="bibtex">
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29
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193 @article{Huang1999,
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194 journal = {Genome Research},
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195 author = {5. Huang X, Madan A},
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28
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196 title = {CAP3: A DNA sequence assembly program},
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197 year = {1999},
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198 volume = {9},
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199 number = {9},
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29
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200 pages = {868-877},
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201 url = {http://seq.cs.iastate.edu/cap3.html},}
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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{Eddy2009,
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205 journal = {Genome Inform},
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206 author = {6. Eddy SR},
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28
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207 title = {A new generation of homology search tools based on probabilistic inference},
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208 year = {2009},
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209 volume = {23},
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210 number = {1},
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29
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211 pages = {205-211},}
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28
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212 </citation>
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213 <citation type="bibtex">
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30
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214 @article{Katoh2013,
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215 journal = {Molecular biology and evolution},
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216 author = {7. Katoh K, Standley DM},
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217 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
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218 year = {2013},
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219 volume = {30},
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220 number = {4},
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221 pages = {772-780},}
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222 </citation>
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223 <citation type="bibtex">
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29
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224 @article{Sasidharan2012,
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225 journal = {Nucleic Acids Research},
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30
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226 author = {8. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
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28
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227 title = {GFam: a platform for automatic annotation of gene families},
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228 year = {2012},
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29
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229 pages = {gks631},}
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28
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230 </citation>
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231 <citation type="bibtex">
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29
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232 @article{Li2003,
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233 journal = {Genome Research}
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30
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234 author = {9. Li L, Stoeckert CJ, Roos DS},
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28
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235 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
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236 year = {2003},
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237 volume = {13},
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238 number = {9},
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29
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239 pages = {2178-2189},}
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28
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240 </citation>
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241 <citation type="bibtex">
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29
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242 @article{Emms2015,
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243 journal = {Genome Biology}
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30
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244 author = {10. Emms DM, Kelly S},
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28
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245 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
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246 year = {2015},
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247 volume = {16},
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248 number = {1},
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29
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249 pages = {157},}
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28
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250 </citation>
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251 <citation type="bibtex">
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29
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252 @article{Capella-Gutierrez2009,
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253 journal = {Bioinformatics,},
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30
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254 author = {11. Capella-Gutierrez S, Silla-MartÃnez JM, Gabaldón T},
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28
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255 title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
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256 year = {2009},
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257 volume = {25},
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258 number = {15},
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29
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259 pages = {1972-1973},}
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28
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260 </citation>
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261 <citation type="bibtex">
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29
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262 @article{Gremme2013,
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263 journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
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30
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264 author = {12. Gremme G, Steinbiss S, Kurtz S},
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28
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265 title = {GenomeTools: a comprehensive software library for efficient processing of structured genome annotations},
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266 year = {2013},
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267 volume = {10},
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268 number = {3},
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29
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269 pages = {645-656},}
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28
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270 </citation>
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24
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271 <citation type="bibtex">
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29
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272 @article{None,
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273 journal = {GitHub repository},
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30
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274 author = {13. None},
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24
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275 title = {HMMER 3.1+ hmmscan search sequence(s) against a profile database},
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276 year = {2013},
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29
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277 url = {http://hmmer.org},}
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28
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278 </citation>
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0
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279 </citations>
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280 </tool>
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29
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281
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