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annotate pairwise.xml @ 0:e95d4b20c62d draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
author abims-sbr
date Thu, 13 Apr 2017 05:46:29 -0400
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children 5f68b2fc02c1
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e95d4b20c62d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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1 <?xml version="1.0"?>
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3 <tool name="Pairwise" id="pairwise" version="1.0">
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5 <description>
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6 Run reciproque tblastx pairwise
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7 </description>
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9 <macros>
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10 <import>macros.xml</import>
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11 </macros>
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13 <requirements>
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14 <expand macro="python_required" />
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15 <requirement type="package" version="2.2.22">blast-legacy</requirement>
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16 <requirement type="package" version="1.3.1">samtools</requirement>
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17 </requirements>
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19 <command>
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20 <![CDATA[
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21 ln -s $__tool_directory__/scripts/S02_xxx_patron_pipeline.sh .
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22 &&
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23 ln -s $__tool_directory__/scripts/S03_run_blast_with_k_filter.sh .
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24 &&
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25 ln -s $__tool_directory__/scripts/S04_run_blast2_with_k_filter.sh .
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26 &&
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27 ln -s $__tool_directory__/scripts/S05_script_extract_match_v20_blastx.py .
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28 &&
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29 ln -s $__tool_directory__/scripts/S06_post_processing_of_pairwise.py .
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30 &&
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31 ln -s $__tool_directory__/scripts/S07_format_match_get_back_nucleotides.py .
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32 &&
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33 ln -s $__tool_directory__/scripts/S08_script_extract_match_v20_blastx.py .
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34 &&
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35 ln -s $__tool_directory__/scripts/S09_post_processing_of_pairwise.py .
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36 &&
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37 ln -s $__tool_directory__/scripts/S10_compare_list_pairs_for_reciprocal_best_hits_test.py .
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38 &&
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39 ln -s $__tool_directory__/scripts/S11_post_processing_of_pairwise.py .
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40 &&
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41 ln -s $__tool_directory__/scripts/S12_prot2dna.py .
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42 &&
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43 ln -s $__tool_directory__/scripts/S13_zip.py .
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44 &&
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45 python $__tool_directory__/scripts/S01_organize_rbh.py 8 ${e_value} ${zip}
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46 > ${output};
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47 ]]>
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48 </command>
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49
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50 <inputs>
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51 <param name="zip" type="data" format="no_unzip.zip,zip" multiple="true" label="Choose your ZIP file" help="Contains the output of the filter tool" />
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52 <param name="e_value" type="float" value="1e-5" label="e_value" help="By default, it's 1e-5. you can write the e-value like this: 1e-5" />
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53 </inputs>
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54
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55 <outputs>
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56 <data format="txt" name="output" label="Pairwise" />
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57 <data format="no_unzip.zip" name="output_zip_DNA" label="Pairwise_zip_DNA" from_work_dir="output_file_DNA.zip" />
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58 <data format="no_unzip.zip" name="output_zip_PROT" label="Pairwise_zip_PROT" from_work_dir="output_file_PROT.zip" />
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59 </outputs>
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60
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61 <tests>
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62 <test>
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63 <param name="zip" ftype="zip" value="test_02_input_pairwise.zip" />
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64 <param name="e-value" value="1e-5" />
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65 <output name="output" >
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66 <assert_contents>
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67 <has_line line="('PfPfiji_Trinity.fasta', 'ApApomp_Trinity.fasta')"/>
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68 <has_line line="('PfPfiji_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/>
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69 <has_line line="('PfPfiji_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
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70 <has_line line="('ApApomp_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/>
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71 <has_line line="('ApApomp_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
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72 <has_line line="('AmAmphi_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
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73
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74 <has_text text="Number of pairwises parsed = 2" />
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75 <has_text text="Number of pairwises parsed = 3" />
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76 <has_text text="Number of pairwises parsed = 0" />
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77 <has_text text="Number of pairwises parsed = 5" />
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78 <has_text text="Number of pairwises parsed = 1" />
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79
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80 </assert_contents>
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81 </output>
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82 </test>
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83 </tests>
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85 <help>
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87 ============
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88 What it does
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89 ============
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90
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91 | This tool takes a zip archive containing nucleic fasta sequence files and searches different homologous genes from pairwise comparaisons.
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92 | There are 3 outputs.
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93 |
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94 | The run blast was written by the **NCBI**.
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95 | The script was written by **Eric Fontanillas**.
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96 | The wrapper was written by **Julie Baffard**.
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97
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98 --------
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99
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100 ==========
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101 Parameters
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102 ==========
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103
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104 The choice of parameters is possible :
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105
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106 **-e** :
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107 | is the option for the choice of the e-value.
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108 | By default it's 10.
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109 |
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110
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111 --------
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112
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113 =======
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114 Outputs
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115 =======
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116
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117 This tool, produces the following files :
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118
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119 **Pairwise** :
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120 | is the general output. It gives the information about what the tool is doing (for each pairwise).
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121 |
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122
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123 **Pairwise_zip_DNA.zip** :
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124 | is the output wich contains nucleic sequences (of the pairwise) that are homologues. The sequences are with nucleotides. Shows :
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125 | the name of the query sequence
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126 | the part of the sequence in nucleotides
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127 | the name of the match sequence
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128 | the part of the sequence in nucleotides
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129 |
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130
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131 **Pairwise_zip_PROT.zip** :
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132 | is the output wich contains proteic sequences (of the pairwise) that are homologues. The sequences are with protein. Shows :
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133 | the name of the query sequence (the name of the sequence || the position (Start and End) of the homologous sequences || divergence || number of gaps || real divergence || the length of the homologous sequence)
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134 | the part of the sequence in protein
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135 | the name of the match sequence (the name of the sequence || the position (Start and End) of the homologous sequences || divergence || number of gaps || real divergence || the length of the homologous sequence)
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136 | the part of the sequence in protein
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137
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138 .. class:: warningmark
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139
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140 The two zip outputs have to be downloaded (and extracts the files with a file archiver software), you cannot visualize them with the "eye icon" through the interface.
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141
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142 --------
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143
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144 ===============
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145 Working Example
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146 ===============
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147
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148 ---------------------------
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149 The input files and options
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150 ---------------------------
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151
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152 **Input files**
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153 | 3 files with 200 nucleic sequences each : Ap.fasta, Ac.fasta et Pp.fasta
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154 |
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155 **Parameters**
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156 | e-value = 1e-20
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157 |
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158
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159 ----------------
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160 The output files
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161 ----------------
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162
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163 **Pairwise**
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164
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165 | -------------------- Pairwise Pp_Ap --------------------
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166 |
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167 | database : Pp.fasta
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168 | query file : Ap.fasta
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169 |
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170 | ***** START run BLAST *****
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171 | ***** END run BLAST *****
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172 |
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173 |
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174 | database : Ap.fasta
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175 | query file : only the sequences of Pp.fasta who matched during the last BLAST
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176 |
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177 | ***** START run BLAST *****
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178 | ***** END run BLAST *****
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179 |
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180 | [3/5] Get pairs of sequences ...
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181 | Get list of fasta name involved in RBH
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182 | Number of pairwises parsed = 15
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183 | Get subset of Alvinella db
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184 | Get subset of Paralvinella db
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185 |
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186 | -------------------- Pairwise Pp_Ac --------------------
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187 |
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188 | database : Pp.fasta
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189 | query file : Ac.fasta
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190 |
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191 | ***** START run BLAST *****
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192 | ***** END run BLAST *****
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193 |
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194 |
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195 | database : Ac.fasta
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196 | query file : only the sequences of Pp.fasta who matched during the last BLAST
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197 |
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198 | ***** START run BLAST *****
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199 | ***** END run BLAST *****
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200 |
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201 | [3/5] Get pairs of sequences ...
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202 | Get list of fasta name involved in RBH
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203 | Number of pairwises parsed = 13
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204 | Get subset of Alvinella db
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205 | Get subset of Paralvinella db
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206 |
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207 |
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208 | -------------------- Pairwise Ap_Ac --------------------
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209 |
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210 | database : Ap.fasta
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211 | query file : Ac.fasta
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212 | 
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213 | ***** START run BLAST *****
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214 | ***** END run BLAST *****
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215 |
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216 |
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217 | database : Ac.fasta
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218 | query file : only the sequences of Ap.fasta who matched during the last BLAST
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219 |
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220 | ***** START run BLAST *****
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221 | ***** END run BLAST *****
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222 |
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223 | [3/5] Get pairs of sequences ...
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224 | Get list of fasta name involved in RBH
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225 | Number of pairwises parsed = 24
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226 | Get subset of Alvinella db
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227 | Get subset of Paralvinella db
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228 |
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229 |
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230
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231 **Pairwise_output_file_PROT**
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232
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233 | Save as *Galaxy{number}-[Pairwise_output_file_PROT].zip*
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234 | If you unzip the file, a number of file appears (number of pairwise) : 19_ReciprocalBestHits_{name_of_pairwise}.fasta
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235 | For example the 4 last sequences of the file 19_ReciprocalBestHits_Pp_Ap.fasta
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236 |
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237 | &gt;Ap123_1/1_1.000_748||254...478||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0
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238 | FVRITVGDEMSRRPKFAMITWVGPEVSPMKRAKVSTDKAFVKQIFQNFAKEIQTSERSELEEEYVRQEVMKAGGA
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239 | &gt;Pp_146_1/2_1.000_713||259...483||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0
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240 | FAYIRCTNEESKRSKFAMITWIGQGVEAMKRAKVSMDKQFLKEIFQNFAREFQTSEKSELDEVCIKHALAIDDGA
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241 | &gt;Ap66_1/1_1.000_400||192...398||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0
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242 | LSTSLLNWRKHTLCF*GMKLILIILLISFIIPAILFLLSIFTTMRMPESREKFRPYECGFDPNHSARTP
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243 | &gt;Pp_201_2/2_1.000_691||14...220||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0
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244 | LSTSLLN*RKQPFASEEMKLLILLLFISALIPRILIILSIFTSIRTPKNREKSSPYECGFDPNHSARTP
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245 |
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246 |
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247
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248 **Pairwise_output_file_DNA**
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249
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250 | Save as *Galaxy{number}-[Pairwise_output_file_DNA].zip*
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251 | If you unzip the file, a number of file appears (number of pairwise) : 25_DNAalignment_corresponding_to_protein_from_19_RBH_{name_of_pairwise}.fasta
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252 | For example the 4 last sequences of the file 25_DNAalignement_corresponding_to_protein_from_19_RBH_Pp_Ap.fasta
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253 |
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254 | &gt;Ap123_1/1_1.000_748
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255 | CCAGTAACAAGCCGCCACGGGTCCGTCGTGTCTTCTCTTCAAGGAAAGGTTGACAGATTCTCGTACGCTAGACGTCGCCACCTACTCGTCCTGGACTCCGGTGCCGTAGGTGGCGCCACCTGCTTTCATCACTTCCTGCCTA
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256 | ACGTACTCCTCTTCTAGCTCCGATCTCTCGCTCGTCTGGATCTCTTTGGCAAAGTTCTGGAATATCTGCTTGACGAACGCCTTGTCCGTGCTGACTTTGGCGCGCTTCATTGGGCTCACTTCCGGTCCGACCCACGTGATCA
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257 | TGGCGAACTTCGGTCTTCTGCTCATTTCGTCCCCGACGGTAATACGGACAAAGGCGAACGCCCGCTGGTCATCTTGTAGTTTTGATAACAGATCCTCGTATTCGGTTCCTGTAGAGTCCAGTATAATATTGTCGCCATCATA
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258 | CGTCACAAACGCCCAGTTTGTCTCCGTCGCGTCGCTCCTGACGTCTTCGTAAGCCTGTCCGATAGCCTCTCTGTCGATGTCTGCCATGCTGCTGGTCCCGCTCTCGACGCTAATGAGCCAATCACGACTTCTGACAGACGAG
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259 | TAGACATGCAGACAGCCAGACGGACTGACGGACTGACG
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260 | &gt;Pp_146_1/2_1.000_713
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261 | CATTAATTGTGTGTCTGGTTGTGGGTGTGTGTTATAAGAGACATCACTTAGTGTATACTGATGTCCACGTGGTAGTTGACCAGCATGTCGAATATGGATAGGGACTCGATCTTGAATGGCTATGAGGAGGTTCGCAACGACGA
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262 | CTCGGACATTAACTGGGCTTTCGTAACGTATTCACCTGACAACAAACTAGTACTTGATTCAACTGGCACAGACTACTTCCAGCTCCAGGAGAAATATCAAGATGATATGCGAGGATTTGCTTACATCCGGTGCACTAACGAGG
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263 | AGAGTAAACGTTCTAAATTTGCCATGATTACCTGGATTGGACAAGGAGTGGAAGCAATGAAGCGTGCCAAGGTCAGCATGGACAAACAGTTCCTAAAGGAAATCTTCCAGAATTTCGCAAGAGAATTTCAGACGAGTGAAAAG
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264 | TCAGAGCTTGATGAGGTCTGTATTAAACACGCGCTTGCCATTGACGATGGAGCTGGTTGCAAAGTGGAAAGCGAGGACACGAGAAAAGGGGCCTTTCTCAGGAAAGAGGATGACACTGAAGTGGAAAGGGAAACTAATGTCAA
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265 | CAATGTCTCCGGTGTCGTGGAAGAAGATGATGACGCAAAAAATGCAAATGATTTTAATTACGAAGAGGACTGTAACAATGAATAGGTGCATGTCGATGATTTATATAGAGAACTAGACTTCGCACTCGCTAGGTGGTTGAT
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266 | &gt;Ap66_1/1_1.000_400
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267 | TGATCGTCTTATAAACCTAACTTGAAAAACCTTCCTACCATTTAGGGCTAGCAGCCCTATTAATTATCACACCTATCGCAGCGCTCTCACTATAATTATAAGTATTGCGCCGGGTTTGAACGGATAGCTCTGATGCTGCTAATT
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268 | ACGGGACCTAATAATCCCCAATACTTTATCCTTAGAGAGCTGTACCTCTTAGCACCAGTCTTTTAAACTGGCGAAAGCACACTTTATGCTTCTAAGGAATGAAACTAATTCTTATAATCCTACTAATCTCTTTTATCATCCCCG
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269 | CCATTCTATTTTTACTCTCGATCTTTACTACTATGCGCATGCCAGAGAGCCGTGAAAAATTTAGGCCCTACGAGTGCGGGTTTGACCCCAATCACTCGGCCCGAACCCCATT
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270 | &gt;Pp_201_2/2_1.000_691
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271 | ATCGTAGGGAAAAAGGTGTTCGTGCAGAATGATTGGGGTCAAATCCACATTCGTAGGGGCTAGATTTTTCACGGTTTTTAGGTGTACGAATAGAGGTGAAGATTGATAGGATGATTAAAATTCTTGGGATTAATGCTGAAATAAA
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272 | GAGAAGTAGGATTAAAAGTTTCATTTCCTCAGAAGCAAAGGGTTGCTTTCGTCAGTTTAAAAGACTGGTGCTAAGTAGGTACAGCTCTCTAAGGG
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273
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274 </help>
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275
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276 <expand macro="citations" />
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277
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278 </tool>