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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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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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68 <param name="scaffold" type="select" label="Gene family 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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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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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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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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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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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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114 <param name="min_length" value="200" />
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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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33
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138 * **Coding regions prediction method** - method for finding coding regions within transcripts. Available methods are TransDecoder[3] and ESTScan[4].
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139 * **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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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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35
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144
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145 * **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, and also available at the PlantTribes github repository (https://github.com/dePamphilis/PlantTribes/tree/master/config).
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146 * **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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147 * **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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148
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33
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149 * **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% of the sequences in the multiple sequence alignment. This option is restricted to the range 0.0 - 1.0.
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150 * **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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151 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
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152 * **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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153
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0
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154 </help>
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155 <citations>
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24
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156 <citation type="bibtex">
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157 @misc{None,
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158 journal = {None},
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159 author = {1. Wafula EK},
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160 title = {Manuscript in preparation},
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161 year = {None},
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162 url = {https://github.com/dePamphilis/PlantTribes},}
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28
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163 </citation>
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164 <citation type="bibtex">
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29
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165 @article{Honaas2016,
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166 journal = {PloS one},
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167 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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168 title = {Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome},
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169 year = {2016},
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170 volume = {11},
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171 number = {1},
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29
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172 pages = {e0146062},}
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28
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173 </citation>
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24
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174 <citation type="bibtex">
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29
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175 @article{Haas2013,
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176 journal = {Nature Protocols},
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177 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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178 title = {De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis},
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179 year = {2013},
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180 volume = {8},
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181 number = {8},
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29
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182 pages = {1494-1512},}
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28
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183 </citation>
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184 <citation type="bibtex">
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29
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185 @article{Iseli1999,
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186 journal = {ISMB},
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187 author = {4. Iseli C, Jongeneel CV, Bucher P},
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188 title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences},
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189 year = {1999},
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28
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190 volume = {99},
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29
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191 pages = {138-148},
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192 url = {http://estscan.sourceforge.net},}
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28
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193 </citation>
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194 <citation type="bibtex">
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29
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195 @article{Huang1999,
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196 journal = {Genome Research},
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197 author = {5. Huang X, Madan A},
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28
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198 title = {CAP3: A DNA sequence assembly program},
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199 year = {1999},
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200 volume = {9},
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201 number = {9},
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29
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202 pages = {868-877},
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203 url = {http://seq.cs.iastate.edu/cap3.html},}
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28
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204 </citation>
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205 <citation type="bibtex">
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29
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206 @article{Eddy2009,
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207 journal = {Genome Inform},
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208 author = {6. Eddy SR},
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28
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209 title = {A new generation of homology search tools based on probabilistic inference},
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210 year = {2009},
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211 volume = {23},
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212 number = {1},
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29
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213 pages = {205-211},}
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28
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214 </citation>
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215 <citation type="bibtex">
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30
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216 @article{Katoh2013,
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217 journal = {Molecular biology and evolution},
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218 author = {7. Katoh K, Standley DM},
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219 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
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220 year = {2013},
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221 volume = {30},
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222 number = {4},
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223 pages = {772-780},}
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224 </citation>
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225 <citation type="bibtex">
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29
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226 @article{Sasidharan2012,
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227 journal = {Nucleic Acids Research},
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30
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228 author = {8. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
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28
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229 title = {GFam: a platform for automatic annotation of gene families},
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230 year = {2012},
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29
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231 pages = {gks631},}
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28
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232 </citation>
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233 <citation type="bibtex">
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29
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234 @article{Li2003,
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235 journal = {Genome Research}
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30
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236 author = {9. Li L, Stoeckert CJ, Roos DS},
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28
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237 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
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238 year = {2003},
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239 volume = {13},
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240 number = {9},
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29
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241 pages = {2178-2189},}
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28
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242 </citation>
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243 <citation type="bibtex">
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29
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244 @article{Emms2015,
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245 journal = {Genome Biology}
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30
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246 author = {10. Emms DM, Kelly S},
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28
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247 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
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248 year = {2015},
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249 volume = {16},
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250 number = {1},
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29
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251 pages = {157},}
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28
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252 </citation>
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253 <citation type="bibtex">
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29
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254 @article{Capella-Gutierrez2009,
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255 journal = {Bioinformatics,},
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30
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256 author = {11. Capella-Gutierrez S, Silla-MartÃnez JM, Gabaldón T},
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28
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257 title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
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258 year = {2009},
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259 volume = {25},
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260 number = {15},
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29
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261 pages = {1972-1973},}
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28
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262 </citation>
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263 <citation type="bibtex">
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29
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264 @article{Gremme2013,
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265 journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
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30
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266 author = {12. Gremme G, Steinbiss S, Kurtz S},
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28
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267 title = {GenomeTools: a comprehensive software library for efficient processing of structured genome annotations},
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268 year = {2013},
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269 volume = {10},
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270 number = {3},
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29
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271 pages = {645-656},}
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28
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272 </citation>
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0
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273 </citations>
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274 </tool>
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