Mercurial > repos > abims-sbr > filter_assemblies

annotate filter_assembly.xml @ 0:7a813e633d1c draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
author abims-sbr
date Fri, 01 Feb 2019 10:22:32 -0500
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children a83562c0719f
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7a813e633d1c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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1 <tool name="Filter assemblies" id="filter_assemblies" version="2.0.3">
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3 <description>
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4 Filter the outputs of 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="python_required" />
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13 <requirement type="package" version="0.0.14">fastx_toolkit</requirement>
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14 <requirement type="package" version="10.2011">cap3</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 = ""
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20 #for $input in $inputs
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21 ln -s '$input' '$input.element_identifier';
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22 #set $infiles = $infiles + $input.element_identifier + ","
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23 #end for
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24 #set $infiles = $infiles[:-1]
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26 ln -s '$__tool_directory__/scripts/S02a_remove_redondancy_from_velvet_oases.py' . &&
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27 ln -s '$__tool_directory__/scripts/S02b_format_fasta_name_trinity.py' . &&
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28 ln -s '$__tool_directory__/scripts/S03_choose_one_variants_per_locus_trinity.py' . &&
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29 ln -s '$__tool_directory__/scripts/S04_find_orf.py' . &&
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30 ln -s '$__tool_directory__/scripts/S05_filter.py' . &&
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32 python '$__tool_directory__/scripts/S01_script_to_choose.py'
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34 '$infiles'
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35 $length_seq_max
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36 $percent_identity
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37 $overlap_length
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38 > ${log}
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39 ]]>
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40 </command>
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41
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42 <inputs>
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43 <param name="inputs" type="data" format="fasta" multiple="true" label="Input files" />
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44 <param name="percent_identity" type="integer" value="100" 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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45 <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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46 <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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47 </inputs>
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48
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49 <outputs>
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50 <collection name="output_fasta" type="list" label="Filter Assemblies outputs">
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51 <discover_datasets pattern="__name_and_ext__" directory="outputs" />
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52 </collection>
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53 <data format="txt" name="log" label="Filter Assemblies Summary"/>
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54 </outputs>
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55
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56 <tests>
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57 <test>
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58 <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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59 <param name="percent_identity" value="100" />
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60 <param name="overlap_length" value="60" />
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61 <param name="length_seq_max" value="100" />
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62 <output name="log" value="trinity_and_velvet_up.output" />
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63 <output_collection name="output_fasta" type="list">
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64 <element name="AcAc_transcriptome_25591" value="velvet_out/AcAc_transcriptome_25591.fasta" />
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65 <element name="ApAp_transcriptome_35099" value="velvet_out/ApAp_transcriptome_35099.fasta" />
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66 <element name="PgPg_transcriptome_90109" value="velvet_out/PgPg_transcriptome_90109.fasta" />
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67 <element name="AcAcaud_trinity" value="trinity_out/AcAcaud_trinity.fasta" />
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68 <element name="AmAmphi_trinity" value="trinity_out/AmAmphi_trinity.fasta" />
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69 <element name="ApApomp_trinity" value="trinity_out/ApApomp_trinity.fasta" />
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70 <element name="PfPfiji_trinity" value="trinity_out/PfPfiji_trinity.fasta" />
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71 </output_collection>
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72 </test>
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73 <test>
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74 <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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75 <param name="percent_identity" value="100" />
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76 <param name="overlap_length" value="60" />
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77 <param name="length_seq_max" value="100" />
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78 <output name="log" value="trinity_up.output" />
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79 <output_collection name="output_fasta" type="list">
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80 <element name="AcAcaud_trinity" value="trinity_out/AcAcaud_trinity.fasta" />
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81 <element name="AmAmphi_trinity" value="trinity_out/AmAmphi_trinity.fasta" />
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82 <element name="ApApomp_trinity" value="trinity_out/ApApomp_trinity.fasta" />
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83 <element name="PfPfiji_trinity" value="trinity_out/PfPfiji_trinity.fasta" />
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84 </output_collection>
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85 </test>
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86 <test>
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87 <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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88 <param name="percent_identity" value="100" />
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89 <param name="overlap_length" value="60" />
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90 <param name="length_seq_max" value="100" />
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91 <output name="log" value="velvet_up.output" />
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92 <output_collection name="output_fasta" type="list">
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93 <element name="AcAc_transcriptome_25591" value="velvet_out/AcAc_transcriptome_25591.fasta" />
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94 <element name="ApAp_transcriptome_35099" value="velvet_out/ApAp_transcriptome_35099.fasta" />
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95 <element name="PgPg_transcriptome_90109" value="velvet_out/PgPg_transcriptome_90109.fasta" />
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96 </output_collection>
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97 </test>
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98
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99 </tests>
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100
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101 <help>
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102
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103 @HELP_AUTHORS@
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104
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105 <![CDATA[
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106
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107 **Description**
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108
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109 This tool reformats Velvet Oases or Trinity assemblies for the AdaptSearch galaxy suite and selects only one variant per gene according to its length and quality check.
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110
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111 ---------
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112
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113 **Input format**
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114
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115 (1) Sequences are in the sequential format:
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116
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117 | >seqname1
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118 | AAAGAGAGACCACATGTCAGTAGC -on one or several lines -
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119 | >seqname2
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120 | AAGGCCTGACCACATGAGTTAAGC -on one or several lines -
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121 | etc ...
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122 |
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123
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124 2) The file name should begin with a two letter abbreviation of the species name (for isntance, 'Ap' if the species is Alvinella pompejana).
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125
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126 **For Velvet Oases assemblies input**
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127
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128 The headers must be as follow : *>Locus_i_Transcript_i/j_Confidence_x.xxx_Length_N* where i is the locus number, j the transcript variant among all versions of the transcript, x.xxx the confidence value and N the length.
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129
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130 **For Trinity assemblies inputs**
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131
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132 The headers must be as follow : *>cj_gj_ij Len=j path=[j:0-j]* where all the j are integers (locus number, transcript variant, length, position...)
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133
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134 **The tool handles the case if input files come from both assemblers (there is no need for input files to be exclusively from one or another assembler).**
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135
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136 ---------
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137
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138 **Parameters**
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139
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140 - 'Input files' : a collection of fasta files (one file per species).
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141 - 'Overlap percent identity cutoff' : cap3 -p parameter : minimum percent identity of an overlap.
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142 must be > 65 ; default : 100.
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143 - 'Overlap length cutoff' (integer) : cap3 -o parameter : minimum length of an overlap (in base pairs).
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144 must be > 15 ; default : 60.
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145 - 'Minimum sequence length' (integer) : only keep sequences which are longer than the specified value.
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146 default : 100.
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147
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148 ---------
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149
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150 **Steps**:
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151
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152 The tool:
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153 1) Modifies the sequence name to add the species abbreviation using the 2 first letters of the name of the transcriptome file : note that each species abbreviation must be unique
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154 2) Selects one allelic sequence from each transcript (c or locus) using the length of the sequence and its level of confidence
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155 3) Selects the best ORF from the sequence between two stop codons
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156 4) Performs a CAP3 from the full set of ORFs to minimize redundancy
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157 5) Retrieves the initial transcript sequences from the remaining set of proceeded ORF sequences
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158
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159 **Outputs**
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160
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161 - 'Filter Assemblies Summary' : the log file.
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162 - 'Filter Assemblies outputs' : the main results.
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163
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164 ---------
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165
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166 **The AdaptSearch Pipeline**
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167
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168 .. image:: adaptsearch_picture_helps.png
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169
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170 ---------
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171
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172 Changelog
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173 ---------
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174
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175 **Version 2.1 - 15/01/2018**
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176
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177 - Input files can be a mix from files coming either from Trinity or Velvet Oases assemblers
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178
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179 **Version 2.0 - 14/04/2017**
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180
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181 - NEW: Replace the zip between tools by Dataset Collection
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182
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183 **Version 1.0 - 13/04/2017**
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184
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185 - TEST: Add funtional test with planemo
7a813e633d1c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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186 - IMPROVEMENT: Use conda dependencies for cap3, fastaformatter and python
7a813e633d1c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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187
7a813e633d1c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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188 ]]>
7a813e633d1c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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189 </help>
7a813e633d1c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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190
7a813e633d1c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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191 </tool>