Mercurial > repos > abims-sbr > filter_assemblies

annotate filter_assembly.xml @ 2:1daa43b4729c 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 10:06:45 -0400
parents 13a9ae9ef940
children ac2fcb9c706a
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1 <tool name="Filter assemblies" id="filter_assemblies" version="2.0">
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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 = $infiles[:-1]
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25
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26 ln -s '$__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 $assembler
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36 $length_seq_max
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37 $percent_identity
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38 $overlap_length
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39 > ${log}
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40 ]]>
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41 </command>
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43 <inputs>
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44 <param name="inputs" type="data" format="fasta" multiple="true" label="Input files" />
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45 <param name="assembler" type="select" label="Which assembler was used?">
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46 <option value="velvet">Velvet Oases</option>
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47 <option value="trinity">Trinity</option>
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48 </param>
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49 <param name="percent_identity" type="integer" value="100" label="Maximum sequence length" help="Cap3 parameter -p N specify overlap percent identity cutoff N &gt; 65 " />
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50 <param name="overlap_length" type="integer" value="60" label="Maximum sequence length" help="Cap3 parameter -o N specify overlap length cutoff &gt; 15 " />
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51 <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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52 </inputs>
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53
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54 <outputs>
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55 <collection name="output_fasta" type="list" label="Filter Assemblies outputs">
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56 <discover_datasets pattern="__name_and_ext__" directory="outputs" />
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57 </collection>
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58 <data format="txt" name="log" label="Filter Assemblies Summary"/>
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59 </outputs>
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61 <tests>
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62 <test>
2
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63 <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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64 <param name="assembler" value="trinity" />
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65 <param name="percent_identity" value="100" />
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66 <param name="overlap_length" value="60" />
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67 <param name="length_seq_max" value="100" />
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68 <output name="log" value="trinity.output" />
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69 <output_collection name="output_fasta" type="list">
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70 <element name="AcAcaud_trinity" value="trinity_out/AcAcaud_trinity.fasta" />
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71 <element name="AmAmphi_trinity" value="trinity_out/AmAmphi_trinity.fasta" />
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72 <element name="ApApomp_trinity" value="trinity_out/ApApomp_trinity.fasta" />
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73 <element name="PfPfiji_trinity" value="trinity_out/PfPfiji_trinity.fasta" />
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74 </output_collection>
0
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75 </test>
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76 <test>
2
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77 <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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78 <param name="assembler" value="velvet" />
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79 <param name="percent_identity" value="100" />
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80 <param name="overlap_length" value="60" />
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81 <param name="length_seq_max" value="100" />
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82 <output name="log" value="velvet.output" />
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83 <output_collection name="output_fasta" type="list">
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84 <element name="AcAc_transcriptome_25591" value="velvet_out/AcAc_transcriptome_25591.fasta" />
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85 <element name="ApAp_transcriptome_35099" value="velvet_out/ApAp_transcriptome_35099.fasta" />
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86 <element name="PgPg_transcriptome_90109" value="velvet_out/PgPg_transcriptome_90109.fasta" />
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87 </output_collection>
0
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88 </test>
2
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90 </tests>
0
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91
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92 <help>
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93
2
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94 @HELP_AUTHORS@
0
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95
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96 ===========
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97 Filter Oase
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98 ===========
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99
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100 -----------
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101 Description
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102 -----------
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103
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104
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105 This script 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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106
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107 --------
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108
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109 ============
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110 Input format
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111 ============
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112
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113
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114 ---------------------------------
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115 For Velvet Oases assemblies input
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116 ---------------------------------
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117
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118 Because of putative changes in the sequence names of the assemblies associated with the upgrade of the Velvet/Oases software, the script will only work if:
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119
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120 (1)sequences are in the sequential format:
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121 | e.g.
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122 | &gt;seqname
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123 | AAAGAGAGAVCACATGTCAGTAGC
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124 | &gt;seqname
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125 | AAAGAGAGAVCACATGTCAGTAGC
2
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126
0
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127 (2)The name of each transcript must start by a species abbreviation of two letters, unique for each assembly. The file name of the assembly file must also begin with these same two letters.
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128
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129 (3)The syntax of the sequence name must be constructed as: &gt;fh1_2/3_4_5 where are the two chosen letters the number of the locus, the transcript variant among all versions of the transcript,the confidence value and the length of the transcript. In this case, the file name should thus begin with fs.
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130
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131 -----------------------------
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132 For Trinity assemblies inputs
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133 -----------------------------
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134
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135 Because of putative changes in the sequence names of the assemblies associated with the upgrade of the Trinity software, the script will only work if:
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136
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137 (1)Sequences are in the sequential format:
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138 | e.g.
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139 | &gt;seqname
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140 | AAAGAGAGAVCACATGTCAGTAGC
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141 | &gt;seqname
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142 | AAAGAGAGAVCACATGTCAGTAGC
2
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143
0
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144 (2)The name of each transcript must start by &gt;comp, e.g. &gt;comp10020 instead of &gt;c10020 or &gt;transcript, etc...
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145
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146 (3)The syntax of the sequence name should avoid spaces and must contain _len:, e.g. &gt;comp1_g1_it1_len:1000_path=[.....]
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147
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148 (4)A suffix of two letters abbreviating the species name must be chosen, e.g. Homo sapiens -&gt; Hs. The file name of the assembly file must begin with this suffix. Each suffix should be unique among the n analyzed transcriptomes.
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149 e.g. if the file name is Hs_trinity_22000_transcripts.fasta with sequences, the suffix abbreviation must be Hs and all sequences must be : &gt;Hs.
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150 Alternatively if the name is: Homosapiens_trinity_22000_transcripts.fasta, the suffix must be thus Ho.
2
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151
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152 ---------------------------------------------------
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153
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154 Changelog
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155 ---------
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156
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157 **Version 2.0 - 14/04/2017**
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158
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159 - NEW: Replace the zip between tools by Dataset Collection
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160
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161
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162 **Version 1.0 - 13/04/2017**
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163
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164 - TEST: Add funtional test with planemo
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165
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166 - IMPROVEMENT: Use conda dependencies for cap3, fastaformatter and python
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167
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168
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169 </help>
0
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170
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171 <expand macro="citations" />
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172
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173 </tool>