Mercurial > repos > abims-sbr > filter_assemblies

annotate filter_assembly.xml @ 3:faadbce1bbd2 draft default tip

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ee0948efcef5f8732f7f32ce37a8127d891d0c64
author abims-sbr
date Thu, 11 Sep 2025 08:27:22 +0000
parents 000dbfafe31d
children
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1 <tool name="Filter assemblies" id="filter_assemblies" version="2.0.6">
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3 <description>
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4 Filter the outputs of Spades, Velvet or Trinity assemblies
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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="python3_required" />
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13 <requirement type="package" version="10.2011">cap3</requirement>
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14 </requirements>
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16 <command>
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17 <![CDATA[
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18 #set $infiles = ""
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19 #for $input in $inputs
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20 ln -s '$input' '$input.element_identifier';
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21 #set $infiles = $infiles + $input.element_identifier + ","
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22 #end for
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23 #set $infiles = $infiles[:-1]
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25 python '$__tool_directory__/scripts/S01_script_to_choose.py'
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27 '$infiles'
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28 $length_seq_max
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29 $percent_identity
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30 $overlap_length
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31 > '${log}'
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32 ]]>
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33 </command>
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35 <inputs>
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36 <param name="inputs" type="data" format="fasta" multiple="true" label="Input files" />
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37 <param name="percent_identity" type="integer" value="90" label="Overlap percent identity cutoff" help="Cap3 parameter (-p N); minimum percent identity of an overlap. The specified value should be more than 65%." />
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38 <param name="overlap_length" type="integer" value="60" label="Overlap length cutoff" help="Cap3 parameter (-o N); minimum length of an overlap (in base pairs). The specified value should be more than 15 base pairs." />
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39 <param name="length_seq_max" type="integer" value="100" label="Minimum sequence length" help="Keep sequences which length is higher than the minimum sequence length " />
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40 </inputs>
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41
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42 <outputs>
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43 <collection name="output_fasta" type="list" label="Filter Assemblies outputs">
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44 <discover_datasets pattern="__name_and_ext__" directory="outputs" />
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45 </collection>
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46 <data format="txt" name="log" label="Filter Assemblies Summary"/>
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47 </outputs>
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49 <tests>
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50 <test>
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51 <param name="inputs" ftype="fasta" value="trinity/Pfiji_trinity.fasta,trinity/Apomp_trinity.fasta,trinity/Amphi_trinity.fasta,trinity/Acaud_trinity.fasta,velvet/Pg_transcriptome_90109.fasta,velvet/Ap_transcriptome_35099.fasta,velvet/Ac_transcriptome_25591.fasta" />
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52 <param name="percent_identity" value="100" />
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53 <param name="overlap_length" value="60" />
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54 <param name="length_seq_max" value="100" />
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55 <output name="log" value="trinity_and_velvet_up.output" />
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56 <output_collection name="output_fasta" type="list">
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57 <element name="AcAc_transcriptome_25591" value="velvet_out/AcAc_transcriptome_25591.fasta" />
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58 <element name="ApAp_transcriptome_35099" value="velvet_out/ApAp_transcriptome_35099.fasta" />
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59 <element name="PgPg_transcriptome_90109" value="velvet_out/PgPg_transcriptome_90109.fasta" />
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60 <element name="AcAcaud_trinity" value="trinity_out/AcAcaud_trinity.fasta" />
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61 <element name="AmAmphi_trinity" value="trinity_out/AmAmphi_trinity.fasta" />
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62 <element name="ApApomp_trinity" value="trinity_out/ApApomp_trinity.fasta" />
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63 <element name="PfPfiji_trinity" value="trinity_out/PfPfiji_trinity.fasta" />
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64 </output_collection>
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65 </test>
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66 <test>
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67 <param name="inputs" ftype="fasta" value="trinity/Pfiji_trinity.fasta,trinity/Apomp_trinity.fasta,trinity/Amphi_trinity.fasta,trinity/Acaud_trinity.fasta" />
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68 <param name="percent_identity" value="100" />
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69 <param name="overlap_length" value="60" />
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70 <param name="length_seq_max" value="100" />
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71 <output name="log" value="trinity_up.output" />
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72 <output_collection name="output_fasta" type="list">
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73 <element name="AcAcaud_trinity" value="trinity_out/AcAcaud_trinity.fasta" />
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74 <element name="AmAmphi_trinity" value="trinity_out/AmAmphi_trinity.fasta" />
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75 <element name="ApApomp_trinity" value="trinity_out/ApApomp_trinity.fasta" />
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76 <element name="PfPfiji_trinity" value="trinity_out/PfPfiji_trinity.fasta" />
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77 </output_collection>
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78 </test>
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79 <test>
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80 <param name="inputs" ftype="fasta" value="velvet/Pg_transcriptome_90109.fasta,velvet/Ap_transcriptome_35099.fasta,velvet/Ac_transcriptome_25591.fasta" />
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81 <param name="percent_identity" value="100" />
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82 <param name="overlap_length" value="60" />
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83 <param name="length_seq_max" value="100" />
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84 <output name="log" value="velvet_up.output" />
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85 <output_collection name="output_fasta" type="list">
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86 <element name="AcAc_transcriptome_25591" value="velvet_out/AcAc_transcriptome_25591.fasta" />
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87 <element name="ApAp_transcriptome_35099" value="velvet_out/ApAp_transcriptome_35099.fasta" />
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88 <element name="PgPg_transcriptome_90109" value="velvet_out/PgPg_transcriptome_90109.fasta" />
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89 </output_collection>
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90 </test>
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91
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92 </tests>
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93
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94 <help>
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95
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96 @HELP_AUTHORS@
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97
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98 <![CDATA[
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99
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100 **Description**
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101
1
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102 This tool runs the CAP3 software on assembly FASTA data, merge singlets and contigs and then reformat headers to allow any assembly tools.
0
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103
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104 ---------
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105
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106 **Input format**
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107
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108 Sequences are in the FASTA format:
0
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109
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110 | >seqname1
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111 | AAAGAGAGACCACATGTCAGTAGC -on one or several lines -
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112 | >seqname2
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113 | AAGGCCTGACCACATGAGTTAAGC -on one or several lines -
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114 | etc ...
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115 |
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116
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117 ---------
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118
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119 **Parameters**
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120
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121 - 'Input files' : a collection of fasta files (one file per species).
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122 - 'Overlap percent identity cutoff' : cap3 -p parameter : minimum percent identity of an overlap.
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123 must be > 65 ; default : 100.
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124 - 'Overlap length cutoff' (integer) : cap3 -o parameter : minimum length of an overlap (in base pairs).
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125 must be > 15 ; default : 60.
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126 - 'Minimum sequence length' (integer) : only keep sequences which are longer than the specified value.
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127 default : 100.
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128
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129 ---------
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130
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131 **Steps**:
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132
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133 The tool:
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134 1) Performs a CAP3 from the full set of ORFs to minimize redundancy
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135 2) Merges singlets and contigs identified by CAP3
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136 3) Reformats headers of the FASTA records by adding a specified prefix (defined from the original filename) and ensures that sequences are on a single line
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137
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138 **Outputs**
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139
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140 - 'Filter Assemblies Summary' : the log file.
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141 - 'Filter Assemblies outputs' : the main results.
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142
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143 ---------
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144
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145 **The AdaptSearch Pipeline**
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146
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147 .. image:: adaptsearch_picture_helps.png
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148
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149 ---------
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150
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151 Changelog
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152 ---------
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153
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154
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155 **Version 2.2 - 07/10/2024**
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156
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157 - Input files can be from any assembly tools
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158
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159 **Version 2.1 - 15/01/2018**
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160
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161 - Input files can be a mix from files coming either from Trinity or Velvet Oases assemblers
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162
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163 **Version 2.0 - 14/04/2017**
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164
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165 - NEW: Replace the zip between tools by Dataset Collection
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166
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167 **Version 1.0 - 13/04/2017**
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168
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169 - TEST: Add funtional test with planemo
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170 - IMPROVEMENT: Use conda dependencies for cap3, fastaformatter and python
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171
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172 ]]>
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173 </help>
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174
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175 </tool>