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1 <tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.0">
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2 <description>aligns gene family sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements_gene_family_aligner" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 #set input_format = $input_format_cond.input_format
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11 #set alignment_method_cond = $input_format_cond.alignment_method_cond
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12 #set alignment_method = $alignment_method_cond.alignment_method
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12
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13 #if str($input_format_cond.input_format) == 'ptortho':
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13
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14 #set output_codon_alignments = False
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12
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15 #else if str($input_format_cond.input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments ) == 'no':
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13
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16 #set output_codon_alignments = False
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12
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17 #else:
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18 #set output_codon_alignments = True
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12
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19 #end if
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20
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21 python $__tool_directory__/gene_family_aligner.py
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22 --alignment_method $alignment_method
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23 #if str($alignment_method) == 'pasta':
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24 --pasta_script_path '$__tool_directory__/run_pasta.py'
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25 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit
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26 #end if
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27 --num_threads \${GALAXY_SLOTS:-4}
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28 #if str($input_format) == 'ptortho':
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29 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
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30 #else:
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31 ## str($input_format) == 'ptorthocs'
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32 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
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33 #if str($input_format_cond.codon_alignments) == 'yes':
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34 --codon_alignments 'true'
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35 #end if
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36 #end if
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12
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37 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
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38 #if str($remove_gappy_sequences) == 'yes':
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39 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
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40 #set trim_type = $trim_type_cond.trim_type
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41 #if str($trim_type) == 'gap_trimming':
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42 --gap_trimming $trim_type_cond.gap_trimming
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43 #else:
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44 ## str($trim_type) == 'automated_trimming'
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45 --automated_trimming 'true'
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46 #end if
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47 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
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48 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
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49 #if str($remove_sequences_with_gaps) == 'yes':
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50 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
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51 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
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52 #if $output_codon_alignments:
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53 --output '$output_aln_filtered_ca'
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54 --output_dir '$output_aln_filtered_ca.files_path'
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55 #else:
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56 --output '$output_aln_filtered'
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57 --output_dir '$output_aln_filtered.files_path'
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58 #end if
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8
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59 #else:
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12
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60 #if $output_codon_alignments:
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61 --output '$output_aln_trimmed_ca'
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62 --output_dir '$output_aln_trimmed_ca.files_path'
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10
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63 #else:
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64 --output '$output_aln_trimmed'
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65 --output_dir '$output_aln_trimmed.files_path'
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10
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66 #end if
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67 #end if
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12
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68 #else:
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69 #if $output_codon_alignments:
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70 --output '$output_aln_ca'
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71 --output_dir '$output_aln_ca.files_path'
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72 #else:
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73 --output '$output_aln'
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74 --output_dir '$output_aln.files_path'
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75 #end if
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76 #end if
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77 ]]>
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78 </command>
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79 <inputs>
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80 <conditional name="input_format_cond">
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81 <param name="input_format" type="select" label="Select type of data to sub sample">
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82 <option value="ptortho">Gene family clusters</option>
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83 <option value="ptorthocs">Gene family clusters with corresponding coding sequences</option>
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84 </param>
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85 <when value="ptortho">
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86 <param name="input_ptortho" format="ptortho" type="data" label="Gene family clusters" />
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87 <expand macro="cond_alignment_method" />
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88 </when>
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89 <when value="ptorthocs">
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90 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Gene family clusters with corresponding coding sequences" />
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91 <expand macro="cond_alignment_method" />
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92 <expand macro="param_codon_alignments" />
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93 </when>
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94 </conditional>
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95 <expand macro="cond_remove_gappy_sequences" />
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96 </inputs>
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97 <outputs>
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98 <data name="output_aln" format="ptalign" label="Aligned gene family sequences on ${on_string}">
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99 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
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100 </data>
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101 <data name="output_aln_ca" format="ptalignca" label="Aligned gene family sequences with codon alignments on ${on_string}">
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102 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
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103 </data>
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104 <data name="output_aln_filtered" format="ptalignfiltered" label="Filtered aligned gene family sequences on ${on_string}">
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105 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter>
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106 </data>
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107 <data name="output_aln_filtered_ca" format="ptalignfilteredca" label="Filtered aligned gene family sequences with codon alignments on ${on_string}">
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108 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter>
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109 </data>
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110 <data name="output_aln_trimmed" format="ptaligntrimmed" label="Trimmed aligned gene family sequences on ${on_string}">
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111 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
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112 </data>
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113 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="Trimmed aligned gene family sequences with codon alignments on ${on_string}">
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114 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
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115 </data>
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116 </outputs>
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117 <tests>
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118 <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.
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119 <test>
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120 </test>
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121 -->
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122 </tests>
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123 <help>
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124 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
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125 analyses of genome-scale gene families and transcriptomes. This tool aligns gene family sequences.
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126
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127 -----
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128
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129 **Required options**
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130
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131 * **Select type of data to sub sample**
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132
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133 - **Gene family clusters** - sequences classified into gene family clusters.
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134 - **Gene family clusters with corresponding coding sequences** - sequences classified into gene family clusters including corresponding coding sequences.
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135
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136 - **Construct orthogroup multiple codon alignments** - construct orthogroup multiple codon alignments.
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137
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138 * **Select method for multiple sequence alignments**
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139
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140 - **MAFFT algorithm** - mafft algorithm.
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141 - **Pasta algorithm** - pasta algorithm.
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142
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143 - **Maximum number of iterations that the PASTA algorithm will execute** - maximum number of iterations that the PASTA algorithm will execute.
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144
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145 **Other options**
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146
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147 * **Remove gappy sequences in alignments**
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148
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149 - **Select process used for gap trimming** - either nucleotide based or using trimAl's ML heuristic trimming approach
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150
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151 - **Nucleotide based**
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152
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153 - **Remove sites in alignments with gaps of**
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154 - **Maximum number of iterations** - maximum number of iterations for iterative orthogroups realignment, trimming and fitering
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155
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156 </help>
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157 <citations>
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158 <expand macro="citation1" />
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159 <expand macro="citations2to4" />
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160 </citations>
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161 </tool>
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