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annotate eden_converter.xml @ 0:a083202dc29d draft

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author bgruening
date Mon, 02 May 2016 16:17:10 -0400
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0
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1 <tool id="eden_sequence_converter" name="Convert" version="@VERSION@">
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2 <description>sequences to graphs</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="python_requirements">
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7 <requirement type="package" version="2.2.5">viennarna</requirement>
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8 <requirement type="package" version="2.1.6">rnashapes</requirement>
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9 </expand>
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10 <expand macro="macro_stdio"/>
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11 <version_command>echo "@VERSION@"</version_command>
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12 <command>
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13 <![CDATA[
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14 python "$eden_converter_script" '$inputs'
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15 ]]>
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16 </command>
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17 <configfiles>
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18 <inputs name="inputs" />
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19 <configfile name="eden_converter_script">
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20 <![CDATA[
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21 import sys
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22 import json
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23 import networkx
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24 from eden.converter.fasta import fasta_to_sequence
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25 from eden.converter.rna.rnashapes import rnashapes_to_eden
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26 from eden.converter.rna.rnafold import rnafold_to_eden
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27 from eden.converter.graph.node_link_data import eden_to_node_link_data
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28 #*from eden.converter.graph.node_link_data import eden_to_node_link_file*#
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29
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30 input_json_path = sys.argv[1]
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31 params = json.load(open(input_json_path, "r"))
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32
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33 sequence_iterable = fasta_to_sequence("$infile")
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34
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35 if "$converter_options.selected_converter" == "rnafold_to_eden":
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36 graph_list = rnafold_to_eden(sequence_iterable)
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37 elif "$converter_options.selected_converter" == "rnashapes_to_eden":
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38 params["converter_options"].pop('selected_converter')
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39 sub_params = params["converter_options"]["options"]
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40 graph_list = rnashapes_to_eden(sequence_iterable, **sub_params )
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41
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42 json_graph_list = eden_to_node_link_data(graph_list)
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43
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44 #*TODO: replace with eden_to_node_link_file(graph_list, fname)*#
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45 with open("$outfile", 'w+') as out_file:
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46 for json_graph in json_graph_list:
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47 out_file.write(json_graph + '\n')
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48 ]]>
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49 </configfile>
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50 </configfiles>
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51 <inputs>
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52 <param name="infile" type="data" format="fasta" label="Fasta file" help="File including lines with FASTA format."/>
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53 <conditional name="converter_options">
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54 <param name="selected_converter" type="select" label="Folding algorithm">
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55 <option value="rnafold_to_eden">RNAfold</option>
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56 <option value="rnashapes_to_eden">RNAshapes</option>
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57 </param>
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58 <when value="rnafold_to_eden">
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59 </when>
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60 <when value="rnashapes_to_eden">
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61 <section name="options" title="Advanced Options" expanded="False">
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62 <param argument="shape_type" type="integer" optional="true" value="5" label="Shape type" help="The level of abstraction or dissimilarity which defines a different shape. ( Integer ranging from 1 to 5; default : 5 )"/>
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63 <param argument="energy_range" type="integer" optional="true" value="10" label="Energy range" help="Energy range as percentage value of the minimum free energy. ( Positive floating point number; default : 10 )"/>
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64 <param argument="max_num" type="integer" optional="true" value="3" label="Number of generated shapes" help="Maximum number of structures that are generated. ( default : 3 )"/>
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65 <param argument="split_components" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Split structures" help="Yields each strucutre as an independent graph or packs all structures in the same graph with several disconnectd components. ( default : False )"/>
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66 </section>
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67 </when>
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68 </conditional>
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69 </inputs>
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70 <outputs>
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71 <data format="json" name="outfile"/>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="infile" value="RF01704.fasta" ftype="fasta"/>
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76 <param name="selected_converter" value="rnafold_to_eden"/>
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77 <output name="outfile" file="converter_result01.json"/>
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78 </test>
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79 <test>
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80 <param name="infile" value="RF01704.fasta" ftype="fasta"/>
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81 <param name="selected_converter" value="rnashapes_to_eden"/>
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82 <param name="shape_type" value="2" />
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83 <param name="energy_range" value="4" />
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84 <param name="max_num" value="3" />
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85 <param name="split_components" value="true" />
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86 <output name="outfile" file="converter_result02.json"/>
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87 </test>
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88 </tests>
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89 <help>
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90 <![CDATA[
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91 **What it does**
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92
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93 This tool transforms fasta sequences to graphs that encode secondary structure information.
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94
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95 Users can choose between two RNA folding algorithms:
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96
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97 1. RNAfold to predict the Minimum Free Energy (mfe) structure.
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98
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99 2. RNAshapes to predict a specified number of shapes with the highest occurrence probability.
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100
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101 ]]>
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102 </help>
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103 <expand macro="eden_citation"/>
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104 </tool>