Mercurial > repos > abims-sbr > pairwise

annotate pairwise.xml @ 9:1e0c547d88fe draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
author abims-sbr
date Tue, 03 Jul 2018 10:52:31 -0400
parents f1ee838a8966
children ae65822c1fb7
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1 <tool name="Pairwise" id="pairwise" version="2.1.1">
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3 <description>
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4 Find homologous couples by blast with RBH
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5 </description>
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7 <macros>
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8 <import>macros.xml</import>
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9 </macros>
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11 <requirements>
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12 <expand macro="python_required" />
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13 <requirement type="package" version="1.65">biopython</requirement>
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14 <requirement type="package" version="0.9.22">diamond</requirement>
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15 <requirement type="package" version="2.2.22">blast-legacy</requirement>
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16 </requirements>
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18 <command><![CDATA[
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19 #set $infiles = ""
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20 #for $input in $inputs
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21 ln -s '$input' '$input.element_identifier';
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22 #set $infiles = $infiles + $input.element_identifier + ","
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23 #end for
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24 #set $infiles = $infiles[:-1]
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26 ln -s $__tool_directory__/scripts/S02_04_keep_one_hit_from_blast.py . &&
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27 ln -s $__tool_directory__/scripts/S03_run_second_blast.py . &&
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28 ln -s $__tool_directory__/scripts/S05_find_rbh.py . &&
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30 python -W ignore $__tool_directory__/scripts/S01_run_first_blast.py $infiles ${e_value} $method
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31 > ${output};
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32 ]]></command>
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34 <inputs>
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35 <param name="inputs" type="data" format="fasta" multiple="true" label="Input fasta files" />
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36 <param name="method" type="select" label="Alignment tool to use" help="tblastx is slow and sensitive, diamond is a lot quicker and less sensitive">
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37 <option value="tblastx">tblastx</option>
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38 <option value="diamond">Diamond</option>
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39 </param>
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40 <param name="e_value" type="float" value="1e-5" label="e_value" help="e-value for blast." />
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41 </inputs>
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43 <outputs>
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44 <data format="txt" name="output" label="Pairwise" />
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45 <collection name="output_fasta_dna" type="list" label="Pairwise_DNA">
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46 <discover_datasets pattern="__name_and_ext__" directory="outputs_RBH_dna" />
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47 </collection>
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48 </outputs>
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49
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50 <tests>
4
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51 <test>
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52 <param name="inputs" ftype="fasta" value="inputs_tblastx/AcAcaud_trinity.fasta,inputs_tblastx/AmAmphi_trinity.fasta,inputs_tblastx/ApApomp_trinity.fasta,inputs_tblastx/PfPfiji_trinity.fasta" />
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53 <param name="e-value" value="1e-5" />
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54 <param name="method" value="tblastx" />
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55 <output_collection name="output_fasta_dna" type="list">
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56 <element name="RBH_AcAcaud_AmAmphi_dna">
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57 <assert_contents>
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58 <has_text text=">Ac5_1/1_1.000_160"/>
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59 <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>
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60 <has_text text=">Am1_1/1_1.000_160"/>
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61 <has_text text=">Ac7_1/1_1.000_160"/>
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62 <has_text text="GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGG"/>
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63 <has_text text=">Am3_1/1_1.000_160"/>
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64 <has_text text=">Ac6_1/1_1.000_160"/>
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65 <has_text text="CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTA"/>
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66 <has_text text=">Am2_1/1_1.000_160"/>
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67 </assert_contents>
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68 </element>
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69 <element name="RBH_AcAcaud_PfPfiji_dna">
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70 <assert_contents>
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71 <has_text text=">Ac8_1/1_1.000_160"/>
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72 <has_text text="ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTG"/>
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73 <has_text text=">Pf8_1/1_1.000_160"/>
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74 <has_text text=">Ac5_1/1_1.000_160"/>
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75 <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCAC"/>
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76 <has_text text=">Pf7_1/1_1.000_160"/>
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77 </assert_contents>
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78 </element>
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79 <element name="RBH_ApApomp_PfPfiji_dna">
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80 <assert_contents>
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81 <has_text text=">Ap2_1/1_1.000_160"/>
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82 <has_text text="ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTA"/>
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83 <has_text text=">Pf5_1/1_1.000_160"/>
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84 <has_text text=">Ap1_1/1_1.000_160"/>
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85 <has_text text="GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAA"/>
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86 <has_text text=">Pf4_1/1_1.000_160"/>
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87 <has_text text=">Ap4_1/1_1.000_135"/>
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88 <has_text text="CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGA"/>
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89 <has_text text=">Pf10_1/1_1.000_160"/>
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90 <has_text text=">Ap3_1/1_1.000_160"/>
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91 <has_text text="GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCT"/>
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92 <has_text text=">Pf6_1/1_1.000_160"/>
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93 </assert_contents>
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94 </element>
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95 <element name="RBH_AmAmphi_PfPfiji_dna">
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96 <assert_contents>
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97 <has_text text=">Am8_1/1_1.000_160"/>
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98 <has_text text="GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCAT"/>
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99 <has_text text=">Pf9_1/1_1.000_160"/>
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100 <has_text text=">Am1_1/1_1.000_160"/>
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101 <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>
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102 <has_text text=">Pf7_1/1_1.000_160"/>
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103 </assert_contents>
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104 </element>
4
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105 </output_collection>
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106 </test>
3
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107
9
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108 <test>
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109 <param name="inputs" ftype="fasta" value="inputs_diamond/AcAcaud_Trinity.fasta,inputs_diamond/AmAmphi_Trinity.fasta,inputs_diamond/ApApomp_Trinity.fasta,inputs_diamond/PfPfiji_Trinity.fasta" />
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110 <param name="e-value" value="1e-5" />
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111 <param name="method" value="diamond" />
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112 <output_collection name="output_fasta_dna" type="list">
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113 <element name="RBH_AcAcaud_AmAmphi_dna">
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114 <assert_contents>
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115 <has_text text=">Ac5_1/1_1.000_160"/>
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116 <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>
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117 <has_text text=">Am1_1/1_1.000_160"/>
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118 <has_text text=">Ac7_1/1_1.000_160"/>
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119 <has_text text="GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGG"/>
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120 <has_text text=">Am3_1/1_1.000_160"/>
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121 <has_text text=">Ac6_1/1_1.000_160"/>
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122 <has_text text="CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTA"/>
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123 <has_text text=">Am2_1/1_1.000_160"/>
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124 </assert_contents>
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125 </element>
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126 <element name="RBH_AcAcaud_ApApomp_dna">
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127 <assert_contents>
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128 <has_text text=">Ac23_1/1_1.000_366"/>
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129 <has_text text="ACTGAGGCTCGAACACAACAAAAAGGTGATGAGCAGTCAGCACTTAATAGAATATTACAGCAAGTAGCCAGTAA"/>
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130 <has_text text=">Ap46_1/1_1.000_217"/>
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131 <has_text text="CCACAACCAAGTGGCGGGTATAACAGCACCGAGGCTCGAACACAGCAAAAAGGTGATGAGCAGTCAGCTCTTAA"/>
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132 </assert_contents>
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133 </element>
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134 <element name="RBH_AcAcaud_PfPfiji_dna">
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135 <assert_contents>
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136 <has_text text=">Ac8_1/1_1.000_160"/>
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137 <has_text text="ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTG"/>
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138 <has_text text=">Pf8_1/1_1.000_160"/>
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139 <has_text text=">Ac5_1/1_1.000_160"/>
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140 <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCAC"/>
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141 <has_text text=">Pf7_1/1_1.000_160"/>
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142 </assert_contents>
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143 </element>
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144 <element name="RBH_AmAmphi_PfPfiji_dna">
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145 <assert_contents>
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146 <has_text text=">Am8_1/1_1.000_160"/>
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147 <has_text text="GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCAT"/>
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148 <has_text text=">Pf9_1/1_1.000_160"/>
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149 <has_text text=">Am1_1/1_1.000_160"/>
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150 <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>
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151 <has_text text=">Pf7_1/1_1.000_160"/>
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152 </assert_contents>
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153 </element>
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154 <element name="RBH_ApApomp_PfPfiji_dna">
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155 <assert_contents>
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156 <has_text text=">Ap2_1/1_1.000_160"/>
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157 <has_text text="ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTA"/>
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158 <has_text text=">Pf5_1/1_1.000_160"/>
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159 <!--
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160 <has_text text=">Ap1_1/1_1.000_160"/>
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161 <has_text text="GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAA"/>
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162 <has_text text=">Pf4_1/1_1.000_160"/>
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163 <has_text text=">Ap4_1/1_1.000_160"/>
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164 <has_text text="CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGA"/>
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165 <has_text text=">Pf10_1/1_1.000_160"/>
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166 <has_text text=">Ap3_1/1_1.000_160"/>
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167 <has_text text="GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCT"/>
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168 <has_text text=">Pf6_1/1_1.000_160"/>
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169 -->
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170 </assert_contents>
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171 </element>
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172 </output_collection>
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173 </test>
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174 </tests>
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175
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176 <help>
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177
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178 @HELP_AUTHORS@
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179
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180 <![CDATA[
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181
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182 **Description**
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183
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184 This tool searches for different homologous genes from pairwise comparisons between a set of fasta files (one file per species).
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185
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186 --------
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187
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188 **Parameters**
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189
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190 - 'Input files' : a collection of fasta files (one file per species)
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191 - 'e_value' : the blast e-value. By default it's 1e-5.
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192 - 'Alignment tool' : choose the sequences alignment tool between tblastx and Diamond. tblastx is more sensitive and Diamond is much faster.
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193
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194 --------
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195
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196 **Outputs**
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197
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198 - 'Pairwise' : the general output. It gives the information about what the tool has done for each pairwise.
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199
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200 - 'Pairwise_DNA' : the output which contains nucleic sequences (of the pairwise) that are homologous. The sequences are with nucleotides. It shows for both the query and match :
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201 the name
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202 the sequence in nucleotides
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203
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204 --------
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205
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206 **The AdaptSearch Pipeline**
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207
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208 .. image:: adaptsearch_picture_helps.png
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209
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210 ---------
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211
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212 Changelog
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213 ---------
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214
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215 **Version 2.1 - 03/07/2018**
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216
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217 - Add the possibility to use Diamond instead of tblastx
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218
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219 **Version 2.0 - 18/04/2017**
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220
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221 - NEW: Replace the zip between tools by Dataset Collection
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222
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223
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224 **Version 1.0 - 13/04/2017**
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225
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226 - TEST: Add functional test with planemo
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228 - IMPROVEMENT: Use conda dependencies for blast, samtools and python
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229
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230 ]]>
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231 </help>
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233 <expand macro="citations" />
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235 </tool>