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annotate POGs.xml @ 5:dad7053ba20e draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
author abims-sbr
date Wed, 27 Sep 2017 10:02:20 -0400
parents b7bd93fc0ac9
children b19ed7395dcc
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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 </requirements>
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15 <command>
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16 <![CDATA[
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17 #set $infiles_from_filter_assembly = ""
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18 #for $input_from_filter_assembly in $inputs_from_filter_assembly
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19 ln -s '$input_from_filter_assembly' '$input_from_filter_assembly.element_identifier';
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20 #set $infiles_from_filter_assembly = $infiles_from_filter_assembly + $input_from_filter_assembly.element_identifier + ","
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21 #end for
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22 #set $infiles_from_filter_assembly = $infiles_from_filter_assembly[:-1]
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24 #set $infiles_from_paiwise_prot = ""
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25 #for $input_from_paiwise_prot in $inputs_from_paiwise_prot
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26 ln -s '$input_from_paiwise_prot' '$input_from_paiwise_prot.element_identifier';
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27 #set $infiles_from_paiwise_prot = $infiles_from_paiwise_prot + $input_from_paiwise_prot.element_identifier + ","
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28 #end for
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29 #set $infiles_from_paiwise_prot = $infiles_from_paiwise_prot[:-1]
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31 python '$__tool_directory__/scripts/S01_get_locus_orthologs_part1.py' '$infiles_from_paiwise_prot'
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32 > ${log} &&
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34 python '$__tool_directory__/scripts/S02_get_locus_orthologs_part2.py' '$infiles_from_filter_assembly' $minseq $paralogs
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35 >> ${log};
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36 ]]>
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37 </command>
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39 <inputs>
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40 <param name="inputs_from_filter_assembly" type="data" format="fasta" multiple="true" label="Input files from Filter assemblies" />
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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="minseq" type="integer" value="3" label="Drop orthogroups with less than n species" />
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43 <param name="paralogs" type="select" label="Paralogs savage removal" help="Yes : orthogroups with paralogs will be fully removed. No : paralogs sequences will be (naively) filtered to keep only one sequence." >
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44 <option value="yes">Yes</option>
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45 <option value="no">No</option>
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46 </param>
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47 </inputs>
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49 <outputs>
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50 <data format="txt" name="log" label="POGs" />
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51 <collection name="output" type="list" label="POGs locus orthologs unaligned">
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52 <discover_datasets pattern="__name_and_ext__" directory="outputs" />
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53 </collection>
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54 </outputs>
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56 <tests>
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57 <test>
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58 <param name="inputs_from_filter_assembly" ftype="fasta" value="inputs_from_filter_assembly/PfPfiji_Trinity.fasta,inputs_from_filter_assembly/ApApomp_Trinity.fasta,inputs_from_filter_assembly/AmAmphi_Trinity.fasta,inputs_from_filter_assembly/AcAcaud_Trinity.fasta" />
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59 <param name="inputs_from_paiwise_prot" ftype="fasta" value="inputs_from_paiwise_prot/ReciprocalBestHits_AmAmphi_AcAcaud.fasta,inputs_from_paiwise_prot/ReciprocalBestHits_ApApomp_AcAcaud.fasta,inputs_from_paiwise_prot/ReciprocalBestHits_ApApomp_AmAmphi.fasta,inputs_from_paiwise_prot/ReciprocalBestHits_PfPfiji_AcAcaud.fasta,inputs_from_paiwise_prot/ReciprocalBestHits_PfPfiji_AmAmphi.fasta,inputs_from_paiwise_prot/ReciprocalBestHits_PfPfiji_ApApomp.fasta" />
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60 <param name="minseq" value="2" />
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61 <param name="paralogs" value="no" />
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62 <output name="log" value="pogs.output" />
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63 <output_collection name="output" type="list">
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64 <element name="locus1_sp2" value="outputs_pogs_no/locus1_sp2.fasta" />
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65 <element name="locus1_sp3" value="outputs_pogs_no/locus1_sp3.fasta" />
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66 <element name="locus2_sp2" value="outputs_pogs_no/locus2_sp2.fasta" />
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67 <element name="locus3_sp2" value="outputs_pogs_no/locus3_sp2.fasta" />
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68 <element name="locus4_sp2" value="outputs_pogs_no/locus4_sp2.fasta" />
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69 <element name="locus5_sp2" value="outputs_pogs_no/locus5_sp2.fasta" />
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70 <element name="locus6_sp2" value="outputs_pogs_no/locus6_sp2.fasta" />
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71 <element name="locus7_sp2" value="outputs_pogs_no/locus7_sp2.fasta" />
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72 <element name="locus8_sp2" value="outputs_pogs_no/locus8_sp2.fasta" />
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73 <element name="locus9_sp2" value="outputs_pogs_no/locus9_sp2.fasta" />
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74 <element name="locus10_sp2" value="outputs_pogs_no/locus10_sp2.fasta" />
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75 </output_collection>
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76 </test>
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77 <test>
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78 <param name="inputs_from_filter_assembly" ftype="fasta" value="inputs_from_filter_assembly/PfPfiji_Trinity.fasta,inputs_from_filter_assembly/ApApomp_Trinity.fasta,inputs_from_filter_assembly/AmAmphi_Trinity.fasta,inputs_from_filter_assembly/AcAcaud_Trinity.fasta" />
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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79 <param name="inputs_from_paiwise_prot" ftype="fasta" value="inputs_from_paiwise_prot/ReciprocalBestHits_AmAmphi_AcAcaud.fasta,inputs_from_paiwise_prot/ReciprocalBestHits_ApApomp_AcAcaud.fasta,inputs_from_paiwise_prot/ReciprocalBestHits_ApApomp_AmAmphi.fasta,inputs_from_paiwise_prot/ReciprocalBestHits_PfPfiji_AcAcaud.fasta,inputs_from_paiwise_prot/ReciprocalBestHits_PfPfiji_AmAmphi.fasta,inputs_from_paiwise_prot/ReciprocalBestHits_PfPfiji_ApApomp.fasta" />
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80 <param name="minseq" value="2" />
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81 <param name="paralogs" value="yes" />
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82 <output name="log" value="pogs_para.output" />
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83 <output_collection name="output" type="list">
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84 <element name="locus1_sp2" value="outputs_pogs_yes/locus1_sp2.fasta" />
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85 <element name="locus1_sp3" value="outputs_pogs_yes/locus1_sp3.fasta" />
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86 <element name="locus2_sp2" value="outputs_pogs_yes/locus2_sp2.fasta" />
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87 <element name="locus3_sp2" value="outputs_pogs_yes/locus3_sp2.fasta" />
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88 <element name="locus4_sp2" value="outputs_pogs_yes/locus4_sp2.fasta" />
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89 <element name="locus5_sp2" value="outputs_pogs_yes/locus5_sp2.fasta" />
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90 <element name="locus6_sp2" value="outputs_pogs_yes/locus6_sp2.fasta" />
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91 <element name="locus7_sp2" value="outputs_pogs_yes/locus7_sp2.fasta" />
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92 <element name="locus8_sp2" value="outputs_pogs_yes/locus8_sp2.fasta" />
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93 <element name="locus9_sp2" value="outputs_pogs_yes/locus9_sp2.fasta" />
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94 <element name="locus10_sp2" value="outputs_pogs_yes/locus10_sp2.fasta" />
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95 </output_collection>
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96 </test>
0
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97 </tests>
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98
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99 <help>
5
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100
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101 @HELP_AUTHORS@
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102
0
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103 ============
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104 What it does
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105 ============
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106
5
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107 | This tool parses homologous sequences obtained by pairwise and gather sequences into groups of orthologous sequences.
0
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108 | There are 2 outputs.
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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 Inputs
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114 ======
5
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115 | A dataset collection with the the pairwise with the homologous sequences (obtained from the tool "Pairwise").
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116 | A dataset collection with the fasta sequences of each species (obtained from the tool "Filter_Assemblies")
0
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117
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118 --------
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119
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120 =======
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121 Outputs
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122 =======
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123
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124 This tool, produces the following files :
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125
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126 **POGs** :
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127
5
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128 | is the general output. It gives the number of sequences at each filtering step and then count
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129 | the number of groups.
0
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130
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131 **POGs_locus_orthologs_unaligned** :
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132
5
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133 | is the output which contains the groups of orthologous sequences,
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134 | one file corresponding to one group.
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135
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136 the sequences of each group are in nucleic format.
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137
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138
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139 ===============
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140 Working Example
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141 ===============
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142
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143 ---------------
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144 The input files
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145 ---------------
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146
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147 | 4 simulated files with a few nucleic sequences each : Ac.fasta Am.fasta Ap.fasta Pf.fasta.
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148 | 6 files containing the homologous sequences of each pairwise.
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149
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150 ----------------
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151 The output files
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152 ----------------
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153
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154 **POGs**
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155
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156
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157 | Number of locus before removeRedondancy = 11
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158
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159
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160 | Number of locus = 11
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161
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162
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163 | NUMBER OF REMAINING LOCUS AFTER INTRA LOCUS TREATMENT [REMOVE GROUPS WITH PARALOGS] = 11
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164 | NUMBER OF REMAINING LOCUS AFTER 2ND TREATMENT [INTER LOCUS] = 11
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165
0
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166
5
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167 | REMOVAL OF LOCUS WITH LESS THAN 2 SEQUENCES
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168
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169 | Number of species in the locus : 4
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170 Number of locus : 0
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171
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172 | Number of species in the locus : 3
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173 Number of locus : 1
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174
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175 | Number of species in the locus : 2
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176 Number of locus : 10
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177
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178 **POGs_locus_orthologs_unaligned**
0
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179
5
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180 | For example the file locus1_sp2.fasta :
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181 | &gt;Ac7_1/1_1.000_160
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182 | GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG
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183 | &gt;Am3_1/1_1.000_160
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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184 GCACCTAGAATTACCCGAAGCTTCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGGTGGAAGAAGGCATGTGGTACCATTGGGGTGGTACAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGGAGCAGTTTGACCTTGAGCACCAAG
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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185 ---------------------------------------------------
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186
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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187 Changelog
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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188 ---------
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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189
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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190 **Version 2.0 - 11/07/2017**
0
b2895c835ea8 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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191
5
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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192 - Replace the zip between tools by Dataset Collection
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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193 - Add option : paralogs filtering
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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194 - Added a second functional test (to test the new option)
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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195 - Code factoring
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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196 - Removed zip format of input and output files ; replaced by dataset collections
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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197
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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198
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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199 **Version 1.0 - 13/04/2017**
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200
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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201 - TEST: Add funtional test with planemo
dad7053ba20e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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202 - IMPROVEMENT: Use conda dependencies for python
0
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203
b2895c835ea8 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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204 </help>
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205
b2895c835ea8 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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206 <expand macro="citations" />
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207
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208 </tool>