Mercurial > repos > abims-sbr > pogs

annotate POGs.xml @ 7:04422117fcd7 draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 76e603ecd0118c8060d972b675a13db858956eb6
author abims-sbr
date Wed, 17 Jan 2018 11:31:30 -0500
parents b19ed7395dcc
children 3fbf4e4d111e
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1 <tool name="POGs" id="POGs" version="2.0">
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3 <description>
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4 Find orthologous groups
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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="0.20.0">pandas</requirement>
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14 <requirement type="package" version="1.12.0">numpy</requirement>
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15 </requirements>
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17 <command>
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18 <![CDATA[
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19 #set $infiles_from_paiwise_prot = ""
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20 #for $input_from_paiwise_prot in $inputs_from_paiwise_prot
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21 ln -s '$input_from_paiwise_prot' '$input_from_paiwise_prot.element_identifier';
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22 #set $infiles_from_paiwise_prot = $infiles_from_paiwise_prot + $input_from_paiwise_prot.element_identifier + ","
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23 #end for
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24 #set $infiles_from_paiwise_prot = $infiles_from_paiwise_prot[:-1]
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26 python '$__tool_directory__/scripts/pogs.py' '$infiles_from_paiwise_prot' '$minspec'
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28 #if '$verbose':
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29 -v
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30 #end if
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31 #if '$paralogs':
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32 -p
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33 #end if
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35 > ${log}
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37 ]]>
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38 </command>
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40 <inputs>
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41 <param name="inputs_from_paiwise_prot" type="data" format="fasta" multiple="true" label="Input files from Pairwise Prot" />
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42 <param name="minspec" type="integer" value="3" label="Drop orthogroups with less than n species" />
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43 <param name="verbose" type="boolean" checked="True" truevalue="T" falsevalue="F" label="Verbose" help="Display a summary table of orthogroups before paralogs filtering"/>
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44 <param name="paralogs" type="boolean" checked="False" truevalue="T" falsevalue="F" label="Paralogs" help="Return also orthogroups without paralogs filtering"/>
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45 </inputs>
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47 <outputs>
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48 <data format="txt" name="log" label="pogs.output" />
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49 <collection name="output" type="list" label="POGs_unaligned">
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50 <discover_datasets pattern="__name_and_ext__" directory="outputs" />
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51 </collection>
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52 <collection name="outputPara" type="list" label="POGs_withParalogs_unaligned">
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53 <discover_datasets pattern="__name_and_ext__" directory="outputs_withParalogs" />
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54 <filter>paralogs == True</filter>
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55 </collection>
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56 </outputs>
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58 <tests>
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59 <test>
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60 <param name="inputs_from_paiwise_prot" ftype="fasta" value="output_pairwise/RBH_AmAmphi_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_AcAcaud.fasta,output_pairwise/RBH_TeTerlap_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_ApApomp.fasta"/>
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61 <param name="minspec" value="3"/>
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62 <param name="verbose" value="True"/>
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63 <param name="paralogs" value="True"/>
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64 <output name="log" value="pogs.output" />
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65 <output_collection name="output" type="list">
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66 <element name="orthogroup_1_with_4_sequences" value="outputs/orthogroup_1_with_4_sequences.fasta" />
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67 <element name="orthogroup_2_with_4_sequences" value="outputs/orthogroup_2_with_4_sequences.fasta" />
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68 <element name="orthogroup_3_with_3_sequences" value="outputs/orthogroup_3_with_3_sequences.fasta" />
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69 <element name="orthogroup_4_with_4_sequences" value="outputs/orthogroup_4_with_4_sequences.fasta" />
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70 <element name="orthogroup_5_with_3_sequences" value="outputs/orthogroup_5_with_3_sequences.fasta" />
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71 <element name="orthogroup_6_with_4_sequences" value="outputs/orthogroup_6_with_4_sequences.fasta" />
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72 <element name="orthogroup_7_with_3_sequences" value="outputs/orthogroup_7_with_3_sequences.fasta" />
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73 <element name="orthogroup_8_with_3_sequences" value="outputs/orthogroup_8_with_3_sequences.fasta" />
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74 <element name="orthogroup_9_with_3_sequences" value="outputs/orthogroup_9_with_3_sequences.fasta" />
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75 <element name="orthogroup_10_with_3_sequences" value="outputs/orthogroup_10_with_3_sequences.fasta" />
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76 </output_collection>
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77 <output_collection name="outputPara" type="list">
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78 <element name="orthogroup_1_with_13_sequences_withParalogs" value="outputs_withParalogs/orthogroup_1_with_13_sequences_withParalogs.fasta" />
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79 <element name="orthogroup_2_with_7_sequences_withParalogs" value="outputs_withParalogs/orthogroup_2_with_7_sequences_withParalogs.fasta" />
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80 <element name="orthogroup_3_with_3_sequences_withParalogs" value="outputs_withParalogs/orthogroup_3_with_3_sequences_withParalogs.fasta" />
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81 <element name="orthogroup_4_with_7_sequences_withParalogs" value="outputs_withParalogs/orthogroup_4_with_7_sequences_withParalogs.fasta" />
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82 <element name="orthogroup_5_with_3_sequences_withParalogs" value="outputs_withParalogs/orthogroup_5_with_3_sequences_withParalogs.fasta" />
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83 <element name="orthogroup_6_with_4_sequences_withParalogs" value="outputs_withParalogs/orthogroup_6_with_4_sequences_withParalogs.fasta" />
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84 <element name="orthogroup_7_with_3_sequences_withParalogs" value="outputs_withParalogs/orthogroup_7_with_3_sequences_withParalogs.fasta" />
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85 <element name="orthogroup_8_with_5_sequences_withParalogs" value="outputs_withParalogs/orthogroup_8_with_5_sequences_withParalogs.fasta" />
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86 <element name="orthogroup_9_with_3_sequences_withParalogs" value="outputs_withParalogs/orthogroup_9_with_3_sequences_withParalogs.fasta" />
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87 <element name="orthogroup_10_with_4_sequences_withParalogs" value="outputs_withParalogs/orthogroup_10_with_4_sequences_withParalogs.fasta" />
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88 </output_collection>
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89 </test>
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90 </tests>
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91
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92 <help>
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93
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94 @HELP_AUTHORS@
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95
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96 <![CDATA[
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97
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98 **Last Version** : Victor Mataigne and Gildas Le Corguillé
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99
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100 **Description**
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101
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102 This tool parses homologous sequences obtained by pairwise and gather sequences into groups of orthologous sequences.
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103
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104 --------
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105
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106 **Inputs**
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107
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108 The output (nucleic format) of the tool 'Pairwise' (AdaptSearch suite), which consists in lists of homologous sequences between pairs of species obtained by RBH comparisons.
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109
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110 --------
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111
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112 **Parameters**
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113
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114 ** Species minimum ** : drop orthogroups with less than n species : orthogroups with less than n species within won't be recorded.
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115 ** verbose ** : check 'Yes' if you want a supplementary table : countings of orthogroups before the paralogous sequences removal
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116 ** paralogs ** : check 'yes' if you also want to retrieve the orthogroups before the paralogous sequences removal
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117
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118 .. class:: warningmark
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119 The minimum number of species per group only applies to the main output files. In the case of the 'paralogs' option, this parameter is more likely the minimum amount of sequences to keep.
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120
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121 --------
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122
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123 **Outputs**
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124
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125 This tool, produces the following files :
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126
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127 - POGs : the general output, displaying countings tables of orthogroups.
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128
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129 - POGs_unaligned : a dataset collection which contains the groups of orthologous sequences (one group per file) in nucleic format, with paralogous sequences removed (only one sequence is kept per species and per group)
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130
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131 - POGs_withParalogs_unaligned : a similar dataset colelction in where paralogous sequences are kept. This output is available if you check 'Yes' to the 'paralogous' option.
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132
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133 ---------
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134
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135 **The AdaptSearch Pipeline**
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136
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137 .. image:: adaptsearch_picture_helps.png :heigth: 593 :width: 852
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138
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139 Changelog
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140 ---------
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141
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142 **Version 2.1 - 04/01/2018**
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143
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144 - Rewritten with improved results and better code
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145 - Added options verbose and paralogs
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146
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147 **Version 2.0 - 11/07/2017**
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148
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149 - Replace the zip between tools by Dataset Collection
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150 - Add option : paralogs filtering
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151 - Added a second functional test (to test the new option)
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152 - Code factoring
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153 - Removed zip format of input and output files ; replaced by dataset collections
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154
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155
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156 **Version 1.0 - 13/04/2017**
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157
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158 - TEST: Add funtional test with planemo
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159 - IMPROVEMENT: Use conda dependencies for python
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160
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161 ]]>
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162
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163 </help>
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164
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165 <expand macro="citations" />
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166
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167 </tool>