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annotate pairwise.xml @ 6:af9eb7b4872f draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
author abims-sbr
date Tue, 27 Feb 2018 08:41:20 -0500
parents 6e44f0c3e7c1
children f1ee838a8966
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1 <tool name="Pairwise" id="pairwise" version="2.0.1">
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3 <description>
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4 Run reciproque tblastx pairwise
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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="2.2.22">blast-legacy</requirement>
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14 <requirement type="package" version="1.3.1">samtools</requirement>
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15 </requirements>
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17 <command><![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 ln -s $__tool_directory__/scripts/functions.py . &&
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26 ln -s $__tool_directory__/scripts/S02_xxx_patron_pipeline.sh . &&
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27 ln -s $__tool_directory__/scripts/S03_run_blast_with_k_filter.sh . &&
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28 ln -s $__tool_directory__/scripts/S04_run_blast2_with_k_filter.sh . &&
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29 ln -s $__tool_directory__/scripts/S05_script_extract_match_v20_blastx.py . &&
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30 ln -s $__tool_directory__/scripts/S06_post_processing_of_pairwise.py . &&
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31 ln -s $__tool_directory__/scripts/S07_format_match_get_back_nucleotides.py . &&
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32 ln -s $__tool_directory__/scripts/S08_script_extract_match_v20_blastx.py . &&
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33 ln -s $__tool_directory__/scripts/S09_post_processing_of_pairwise.py . &&
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34 ln -s $__tool_directory__/scripts/S10_compare_list_pairs_for_reciprocal_best_hits_test.py . &&
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35 ln -s $__tool_directory__/scripts/S11_post_processing_of_pairwise.py . &&
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36 ln -s $__tool_directory__/scripts/S12_prot2dna.py . &&
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38 python $__tool_directory__/scripts/S01_organize_rbh.py $infiles ${e_value} \${GALAXY_SLOTS:-1}
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39 > ${output};
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40 ]]></command>
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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="e_value" type="float" value="1e-5" label="e_value" help="By default, it's 1e-5. you can write the e-value like this: 1e-5" />
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45 </inputs>
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47 <outputs>
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48 <data format="txt" name="output" label="Pairwise" />
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49 <collection name="output_fasta_dna" type="list" label="Pairwise DNA">
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50 <discover_datasets pattern="__name_and_ext__" directory="outputs_dna" />
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51 </collection>
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52 <collection name="output_fasta_prot" type="list" label="Pairwise PROT">
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53 <discover_datasets pattern="__name_and_ext__" directory="outputs_prot" />
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54 </collection>
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55 </outputs>
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56
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57 <tests>
4
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58 <test>
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59 <param name="inputs" ftype="fasta" value="inputs2/PfPfiji_trinity.fasta,inputs2/ApApomp_trinity.fasta,inputs2/AmAmphi_trinity.fasta,inputs2/AcAcaud_trinity.fasta" />
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60 <param name="e-value" value="1e-5" />
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61 <output_collection name="output_fasta_dna" type="list">
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62 <element name="DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud" value="outputs_dna2/DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud.fasta" />
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63 <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud" value="outputs_dna2/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud.fasta" />
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64 <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi" value="outputs_dna2/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi.fasta" />
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65 <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp" value="outputs_dna2/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp.fasta" />
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66 </output_collection>
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67 </test>
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68 <test>
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69 <param name="inputs" ftype="fasta" value="inputs/PfPfiji_Trinity.fasta,inputs/ApApomp_Trinity.fasta,inputs/AmAmphi_Trinity.fasta,inputs/AcAcaud_Trinity.fasta" />
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70 <param name="e-value" value="1e-5" />
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71 <output name="output" >
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72 <assert_contents>
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73 <has_line line="('PfPfiji_Trinity.fasta', 'ApApomp_Trinity.fasta')"/>
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74 <has_line line="('PfPfiji_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/>
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75 <has_line line="('PfPfiji_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
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76 <has_line line="('ApApomp_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/>
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77 <has_line line="('ApApomp_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
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78 <has_line line="('AmAmphi_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/>
3
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79
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80 <has_text text="Number of pairwises parsed = 2" />
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81 <has_text text="Number of pairwises parsed = 3" />
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82 <has_text text="Number of pairwises parsed = 0" />
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83 <has_text text="Number of pairwises parsed = 5" />
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84 <has_text text="Number of pairwises parsed = 1" />
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85 </assert_contents>
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86 </output>
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87 <output_collection name="output_fasta_prot" type="list">
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88 <element name="ReciprocalBestHits_AmAmphi_AcAcaud" value="outputs_prot/ReciprocalBestHits_AmAmphi_AcAcaud.fasta" />
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89 <element name="ReciprocalBestHits_ApApomp_AcAcaud" value="outputs_prot/ReciprocalBestHits_ApApomp_AcAcaud.fasta" />
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90 <element name="ReciprocalBestHits_ApApomp_AmAmphi" value="outputs_prot/ReciprocalBestHits_ApApomp_AmAmphi.fasta" />
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91 <element name="ReciprocalBestHits_PfPfiji_AcAcaud" value="outputs_prot/ReciprocalBestHits_PfPfiji_AcAcaud.fasta" />
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92 <element name="ReciprocalBestHits_PfPfiji_AmAmphi" value="outputs_prot/ReciprocalBestHits_PfPfiji_AmAmphi.fasta" />
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93 <element name="ReciprocalBestHits_PfPfiji_ApApomp" value="outputs_prot/ReciprocalBestHits_PfPfiji_ApApomp.fasta" />
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94 </output_collection>
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95 <output_collection name="output_fasta_dna" type="list">
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96 <element name="DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud.fasta" />
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97 <element name="DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AcAcaud.fasta" />
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98 <element name="DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AmAmphi" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AmAmphi.fasta" />
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99 <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud.fasta" />
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100 <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi.fasta" />
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101 <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp.fasta" />
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102 </output_collection>
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103 </test>
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104 </tests>
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105
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106 <help>
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107
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108 @HELP_AUTHORS@
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109
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110 <![CDATA[
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111 ---------
0
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112
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113 **Description**
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114
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115 This tool searches for different homologous genes from pairwise comparisons between a set of fasta files (one file per species).
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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 - 'e_value' : the blast e-value. By default it's 1e-5.
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123
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124 --------
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125
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126 **Outputs**
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127
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128 - 'Pairwise' : the general output. It gives the information about what the tool has done for each pairwise.
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129
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130 - 'Pairwise_DNA' : the output which contains nucleic sequences (of the pairwise) that are homologous. The sequences are with nucleotides. It shows for both the query and match :
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131 the name
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132 the sequence in nucleotides
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133
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134 - 'Pairwise_PROT' : the output which contains proteic sequences (of the pairwise) that are homologous. The sequences are with protein. It shows :
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135 Name, position, length, and part of the sequence in protein for query and match sequences
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136 Divergence
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137 Number of gaps
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138 Real divergence
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139
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140 --------
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141
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142 **The AdaptSearch Pipeline**
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143
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144 .. image:: adaptsearch_picture_helps.png :heigth: 593 :width: 852
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145
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146 ---------
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147
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148 Changelog
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149 ---------
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150
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151 **Version 2.0 - 18/04/2017**
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152
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153 - NEW: Replace the zip between tools by Dataset Collection
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154
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155
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156 **Version 1.0 - 13/04/2017**
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157
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158 - TEST: Add functional test with planemo
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159
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160 - IMPROVEMENT: Use conda dependencies for blast, samtools and python
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161
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162 ]]>
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163 </help>
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164
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165 <expand macro="citations" />
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166
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167 </tool>