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annotate POGs.xml @ 12:752786fe211b draft default tip

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
author lecorguille
date Mon, 24 Sep 2018 03:57:14 -0400
parents 05985273b735
children
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1 <tool name="POGs" id="POGs" version="2.0.1">
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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_dna = ""
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20 #for $input_from_paiwise_dna in $inputs_from_paiwise_dna
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21 ln -s '$input_from_paiwise_dna' '$input_from_paiwise_dna.element_identifier';
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22 #set $infiles_from_paiwise_dna = $infiles_from_paiwise_dna + $input_from_paiwise_dna.element_identifier + ","
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23 #end for
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24 #set $infiles_from_paiwise_dna = $infiles_from_paiwise_dna[:-1]
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26 python '$__tool_directory__/scripts/pogs.py' '$infiles_from_paiwise_dna' '$minspec'
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28 #if $verbose=="T":
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29 -v
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30 #end if
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31 #if $paralogs=="T":
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32 -p
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33 #end if
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35 > ${log}
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36
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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_dna" type="data" format="fasta" multiple="true" label="Input files from Pairwise DNA" />
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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_dna" 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 <test>
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91 <param name="inputs_from_paiwise_dna" 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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92 <param name="minspec" value="3"/>
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93 <param name="verbose" value="True"/>
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94 <param name="paralogs" value="False"/>
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95 <output name="log" value="2_pogs.output" />
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96 <output_collection name="output" type="list">
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97 <element name="orthogroup_1_with_4_sequences" value="outputs/orthogroup_1_with_4_sequences.fasta" />
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98 <element name="orthogroup_2_with_4_sequences" value="outputs/orthogroup_2_with_4_sequences.fasta" />
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99 <element name="orthogroup_3_with_3_sequences" value="outputs/orthogroup_3_with_3_sequences.fasta" />
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100 <element name="orthogroup_4_with_4_sequences" value="outputs/orthogroup_4_with_4_sequences.fasta" />
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101 <element name="orthogroup_5_with_3_sequences" value="outputs/orthogroup_5_with_3_sequences.fasta" />
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102 <element name="orthogroup_6_with_4_sequences" value="outputs/orthogroup_6_with_4_sequences.fasta" />
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103 <element name="orthogroup_7_with_3_sequences" value="outputs/orthogroup_7_with_3_sequences.fasta" />
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104 <element name="orthogroup_8_with_3_sequences" value="outputs/orthogroup_8_with_3_sequences.fasta" />
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105 <element name="orthogroup_9_with_3_sequences" value="outputs/orthogroup_9_with_3_sequences.fasta" />
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106 <element name="orthogroup_10_with_3_sequences" value="outputs/orthogroup_10_with_3_sequences.fasta" />
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107 </output_collection>
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108 </test>
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109 </tests>
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110
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111 <help>
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112
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113 @HELP_AUTHORS@
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114
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115 <![CDATA[
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116
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117 **Description**
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118
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119 This tool parses homologous sequences obtained by pairwise and gather sequences into groups of orthologous sequences.
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120
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121 --------
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122
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123 **Inputs**
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124
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125 The output of the tool 'Pairwise' (pairwise_DNA, nucleic format) (AdaptSearch suite), which consists in lists of homologous sequences between pairs of species obtained by RBH comparisons.
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126
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127 --------
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128
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129 **Parameters**
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130
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131 - Species minimum : drop orthogroups with less than n species : orthogroups with less than n species within won't be recorded.
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132 - verbose : check 'Yes' if you want a supplementary table : countings of orthogroups before the paralogous sequences removal.
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133 - paralogs : check 'Yes' if you also want to retrieve the orthogroups before the paralogous sequences removal.
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134
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135
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136 .. class:: warningmark
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137
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138 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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139
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140 --------
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141
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142 **Outputs**
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143
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144 This tool, produces the following files :
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145
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146 - POGs : the general output, displaying countings tables of orthogroups.
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147
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148 - 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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149
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150 - 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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151
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152 ---------
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153
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154 **The AdaptSearch Pipeline**
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155
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156 .. image:: adaptsearch_picture_helps.png
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157
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158 ---------
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159
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160 Changelog
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161 ---------
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162
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163 **Version 2.1 - 04/01/2018**
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164
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165 - Rewritten with improved results and better code
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166 - Added options verbose and paralogs
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167
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168 **Version 2.0 - 11/07/2017**
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169
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170 - Replace the zip between tools by Dataset Collection
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171 - Add option : paralogs filtering
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172 - Added a second functional test (to test the new option)
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173 - Code factoring
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174 - Removed zip format of input and output files ; replaced by dataset collections
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175
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176
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177 **Version 1.0 - 13/04/2017**
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178
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179 - TEST: Add funtional test with planemo
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180 - IMPROVEMENT: Use conda dependencies for python
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b2895c835ea8 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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b19ed7395dcc planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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182 ]]>
b19ed7395dcc planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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b2895c835ea8 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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184 </help>
b2895c835ea8 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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b2895c835ea8 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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186 </tool>