Mercurial > repos > abims-sbr > cds_search

annotate CDS_search.xml @ 1:c79bdda8abfb draft default tip

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3a118aa934e6406cc8b0b24d006af6365c277519
author abims-sbr
date Thu, 09 Jun 2022 12:40:00 +0000
parents eb95bf7f90ae
children
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1 <tool name="CDS_search" id="cds_search" version="2.2.2">
0
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3 <description>
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4 ORF and CDS search
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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 <requirement type="package" version="1.79">biopython</requirement>
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13 </requirements>
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15 <command><![CDATA[
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16 #for $input in $inputs
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17 ln -s '$input' '$input.element_identifier';
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18 echo '$input.element_identifier' >> list_files;
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19 #end for
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21 ln -s $__tool_directory__/scripts/dico.py . &&
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23 python $__tool_directory__/scripts/S01_find_orf_on_multiple_alignment.py
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24 $__tool_directory__/scripts/code_universel_modified.txt
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25 $length.min_length_seq
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26 $nb_species_keep
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27 list_files
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28 > '$log' &&
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30 python $__tool_directory__/scripts/S02_remove_too_short_bit_or_whole_sequence.py
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31 $nb_species_keep
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32 $methionine
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33 $length.min_length_seq
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34 $length.min_length_subseq
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35 >> '$log' &&
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37 python $__tool_directory__/scripts/S03_remove_site_with_not_enough_species_represented.py
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38 $nb_species_keep
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39 $length.min_length_nuc
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40 >> '$log';
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41 ]]></command>
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42
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43 <inputs>
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44 <param name="inputs" type="data" format="fasta" multiple="true" label="Input files" help="Only a fasta file with nucleic align sequences" />
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45 <!-- <param name="code_file" type="data" format="txt" label="Choose your file containing the universal code (codons and their amino acids)" /> -->
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46
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47 <param name="nb_species_keep" type="integer" value="10" min="2" label="Minimal number of species in each locus" help="If you want to remove all the indels the maximum number of species is required" />
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48
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49 <param name="methionine" type="boolean" checked="true" truevalue="oui" falsevalue="non" label="Do you want to consider the Methionine in the search of CDS? " />
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51 <section name="length" title="Do you want to choose the minimum length of the CDS?">
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52 <param name="min_length_seq" type="integer" value="50" min="0" label="Minimal length of the CDS, in proteic" help="By default it's 50" />
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53 <param name="min_length_subseq" type="integer" value="15" min="0" label="Minimal length of the subsequence, in proteic between two series of indels" help="By default it's 15" />
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54 <param name="min_length_nuc" type="integer" value="50" min="0" label="Minimal length of the CDS, in nucleic without the indel" help="By default it's 50" />
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55 </section>
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56
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57 <param name="out_BESTORF" type="select" label="Do you want the outputs (dataset collection list) containing files with the BEST ORF? ">
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58 <option value="no">No</option>
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59 <option value="aa">Yes, with the proteic format</option>
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60 <option value="nuc">Yes, with the nucleic format</option>
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61 <option value="both">Yes, with the proteic and nucleic format</option>
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62 </param>
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64 <param name="out_CDS" type="select" label="Do you want the outputs (dataset collection list) containing files with CDS? ">
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65 <option value="no">No</option>
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66 <option value="aa">Yes, with the proteic format</option>
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67 <option value="nuc">Yes, with the nucleic format</option>
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68 <option value="both">Yes, with the proteic and nucleic format</option>
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69 </param>
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71 <param name="out_CDS_filter" type="select" label="Do you want the outputs (dataset collection list) containing files with CDS without indel? ">
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72 <option value="no">No</option>
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73 <option value="aa">Yes, with the proteic format</option>
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74 <option value="nuc">Yes, with the nucleic format</option>
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75 <option value="both">Yes, with the proteic and nucleic format</option>
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76 </param>
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77 </inputs>
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79 <outputs>
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80 <data format="txt" name="log" label="ORF_Search" />
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81 <collection name="output_BESTORF_aa" type="list" label="ORF_Search_Best_ORF_aa">
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82 <filter>out_BESTORF in ["aa","both"]</filter>
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83 <discover_datasets pattern="__name_and_ext__" directory="04_BEST_ORF_aa" />
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84 </collection>
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85
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86 <collection name="output_BESTORF_nuc" type="list" label="ORF_Search_Best_ORF_nuc">
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87 <filter>out_BESTORF in ["nuc","both"]</filter>
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88 <discover_datasets pattern="__name_and_ext__" directory="04_BEST_ORF_nuc" />
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89 </collection>
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90
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91 <collection name="output_CDS_aa" type="list" label="ORF_Search_CDS_aa">
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92 <filter>out_CDS in ["aa","both"] and not methionine</filter>
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93 <discover_datasets pattern="__name_and_ext__" directory="05_CDS_aa" />
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94 </collection>
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95
eb95bf7f90ae planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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96 <collection name="output_CDS_nuc" type="list" label="ORF_Search_CDS_nuc">
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97 <filter>out_CDS in ["nuc","both"] and not methionine</filter>
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98 <discover_datasets pattern="__name_and_ext__" directory="05_CDS_nuc" />
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99 </collection>
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100
eb95bf7f90ae planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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101 <collection name="output_CDS_M_aa" type="list" label="ORF_Search_CDS_with_M_aa">
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102 <filter>(out_CDS == "aa" and methionine) or (out_CDS == "both" and methionine)</filter>
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103 <discover_datasets pattern="__name_and_ext__" directory="06_CDS_with_M_aa" />
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104 </collection>
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105
eb95bf7f90ae planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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106 <collection name="output_CDS_M_nuc" type="list" label="ORF_Search_CDS_with_M_nuc">
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107 <filter>(out_CDS == "nuc" and methionine) or (out_CDS == "both" and methionine)</filter>
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108 <discover_datasets pattern="__name_and_ext__" directory="06_CDS_with_M_nuc" />
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109 </collection>
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110
eb95bf7f90ae planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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111 <collection name="output_filter_aa" type="list" label="ORF_Search_CDS_without_indel_aa">
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112 <filter>out_CDS_filter in ["aa","both"]</filter>
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113 <discover_datasets pattern="__name_and_ext__" directory="08_CDS_aa_MINIMUM_MISSING_SEQUENCES" />
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114 </collection>
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115
eb95bf7f90ae planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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116 <collection name="output_filter_nuc" type="list" label="ORF_Search_CDS_without_indel_nuc">
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117 <filter>out_CDS_filter in ["nuc","both"]</filter>
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118 <discover_datasets pattern="__name_and_ext__" directory="08_CDS_nuc_MINIMUM_MISSING_SEQUENCES" />
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119 </collection>
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120 </outputs>
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121
eb95bf7f90ae planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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122 <tests>
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123
eb95bf7f90ae planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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124 <test>
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125 <param name="inputs" ftype="fasta" value="inputs/orthogroup_1_with_4_sequences.fasta,inputs/orthogroup_6_with_4_sequences.fasta,inputs/orthogroup_7_with_3_sequences.fasta,inputs/orthogroup_8_with_4_sequences.fasta,inputs/orthogroup_12_with_5_sequences.fasta,inputs/orthogroup_14_with_4_sequences.fasta" />
eb95bf7f90ae planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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126 <param name="nb_species_keep" value="3" />
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127 <param name="methionine" value="non" />
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128 <section name="length">
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129 <param name="min_length_seq" value="50" />
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130 <param name="min_length_subseq" value="15" />
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131 <param name="min_length_nuc" value="50" />
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132 </section>
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133 <param name="out_BESTORF" value="both" />
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134 <param name="out_CDS" value="both" />
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135 <param name="out_CDS_filter" value="both" />
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136 <output_collection name="output_BESTORF_aa" type="list" count="2">
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137 <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_1_with_3_species.fasta" />
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138 <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_7_with_3_species.fasta" />
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139 </output_collection>
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140 <output_collection name="output_BESTORF_nuc" type="list" count="2">
eb95bf7f90ae planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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141 <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_1_with_3_species.fasta" />
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142 <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_7_with_3_species.fasta" />
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143 </output_collection>
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144 <output_collection name="output_CDS_aa" type="list" count="2">
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145 <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_05_CDS_aa/test1/orthogroup_1_with_3_species.fasta" />
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146 <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_05_CDS_aa/test1/orthogroup_7_with_3_species.fasta" />
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147 </output_collection>
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148 <output_collection name="output_CDS_nuc" type="list" count="2">
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149 <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_1_with_3_species.fasta" />
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150 <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_7_with_3_species.fasta" />
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151 </output_collection>
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152 <output_collection name="output_filter_aa" type="list" count="1">
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153 <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_7_with_3_species.fasta" />
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154 </output_collection>
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155 <output_collection name="output_filter_nuc" type="list" count="1">
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156 <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_7_with_3_species.fasta" />
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157 </output_collection>
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158 </test>
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159
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160 <test>
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161 <param name="inputs" ftype="fasta" value="inputs/orthogroup_1_with_4_sequences.fasta,inputs/orthogroup_6_with_4_sequences.fasta,inputs/orthogroup_7_with_3_sequences.fasta,inputs/orthogroup_8_with_4_sequences.fasta,inputs/orthogroup_12_with_5_sequences.fasta,inputs/orthogroup_14_with_4_sequences.fasta" />
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162 <param name="nb_species_keep" value="2" />
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163 <param name="methionine" value="oui" />
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164 <section name="length">
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165 <param name="min_length_seq" value="50" />
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166 <param name="min_length_subseq" value="15" />
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167 <param name="min_length_nuc" value="50" />
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168 </section>
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169 <param name="out_BESTORF" value="both" />
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170 <param name="out_CDS" value="both" />
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171 <param name="out_CDS_filter" value="both" />
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172 <output_collection name="output_BESTORF_aa" type="list" count="4">
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173 <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_1_with_3_species.fasta" />
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174 <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_6_with_2_species.fasta" />
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175 <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_7_with_3_species.fasta" />
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176 <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_14_with_2_species.fasta" />
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177 </output_collection>
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178 <output_collection name="output_BESTORF_nuc" type="list" count="4">
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179 <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_1_with_3_species.fasta" />
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180 <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_6_with_2_species.fasta" />
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181 <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_7_with_3_species.fasta" />
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182 <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_14_with_2_species.fasta" />
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183 </output_collection>
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184 <output_collection name="output_filter_aa" type="list" count="1">
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185 <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_08_CDS_without_indel_aa/test2/orthogroup_14_with_2_species.fasta" />
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186 </output_collection>
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187 <output_collection name="output_filter_nuc" type="list" count="1">
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188 <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_08_CDS_without_indel_nuc/test2/orthogroup_14_with_2_species.fasta" />
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189 </output_collection>
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190 </test>
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191
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192 </tests>
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193 <help>
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194
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195 @HELP_AUTHORS@
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196
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197 <![CDATA[
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198
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199 **Description**
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200
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201 This tool takes files containing nucleic aligned sequences and search the ORF and the CDS.
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202
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203 --------
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204
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205 **Inputs**
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206
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207 Input files : (multiple) fasta files with nucleic aligned sequences.
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208
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209 --------
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210
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211 **Parameters**
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212
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213 - methionine : choose to consider the methionine in the search of CDS.
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214 yes/no.
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215
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216 - 'Minimal number of species in each locus'
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217 Default : 10 (integer).
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218
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219 - 'min_length_seq' :
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220 minimal length of the sequence (in amino acids).
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221 when the removal of the indel is done, the minimal length equals : previous length - 20.
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222 for example if you choose 50 for the minimal length, the actual length equals 30.
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223 Default : 50 (integer).
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224
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225 - 'min_length_subseq' :
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226 minimal length of the subsequence (in amino acids).
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227 subsequence means the part of the original sequence between 2 sets of indels.
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228 an indel set is composed by more than 2 indels, if not the set is considered as unknown amino acid.
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229 Default : 15 (integer).
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230
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231 - 'min_length_nuc' :
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232 Minimal length of the sequence in the nucleic format, without indels.
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233 Default : 50 (integer).
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234
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235 - others parameters allowing to choose which outputs you desire :
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236 - outputs with best ORFs.
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237 - outputs with CDS, with or without indels.
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238 - in proteic or nucleic format.
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239
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240 --------
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241
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242 **Outputs**
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243
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244 - ORF_Search
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245 the log file (mainly statistics about the tool).
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246
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247 - ORF_Search_Best_ORF_aa
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248 the output with the best ORF in the proteic format.
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249
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250 - ORF_Search_Best_ORF_nuc
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251 the output with the best ORF in the nucleic format.
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252
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253 - ORF_Search_CDS_aa
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254 the output with the CDS (regardless the Methionine) in the proteic format.
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255
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256 - ORF_Search_CDS_nuc
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257 the output with the CDS (regardless the Methionine) in the nucleic format.
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258
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259 - ORF_Search_CDS_with_M_aa
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260 the output with the CDS (considering the Methionine) in proteic format.
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261 the rule : they must have a methionine before the minimal length of the sequence.
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262 for example before the 30 last amino acid.
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263
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264 - ORF_Search_CDS_with_M_nuc
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265 the output with the CDS (considering the Methionine) in nucleic format.
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266 the rule : they must have a methionine before the minimale length of the sequence.
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267 for example before the 30 last amino acid.
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268
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269 - ORF_Search_CDS_without_indel_aa
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270 is the output with the CDS without indel in proteic format.
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271 considering the Methionine or not : according to the option chosen.
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272
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273 - ORF_Search_CDS_without_indel_nuc
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274 is the output with the CDS without indel in proteic format.
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275 considering the Methionine or not : according to the option chosen.
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276
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277 ---------
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278
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279 **The AdaptSearch Pipeline**
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280
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281 .. image:: adaptsearch_picture_helps.png
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282
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283 ---------
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284
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285 Changelog
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286 ---------
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287
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288 **Version 2.0 - 05/07/2017**
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289
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290 - NEW: Replace the zip between tools by Dataset Collection
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291
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292 **Version 1.0 - 13/04/2017**
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293
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294 - Added functional test with planemo
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295 - planemo test with conda dependency for python
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296 - Scripts renamed + symlinks to the directory 'scripts'
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297
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298 ]]>
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299
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300 </help>
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301
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302 <citations>
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303
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304 </citations>
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305
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306 </tool>