view eden_converter.xml @ 0:a083202dc29d draft

planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty

<tool id="eden_sequence_converter" name="Convert" version="@VERSION@">
    <description>sequences to graphs</description>
    <macros>
        <import>main_macros.xml</import>
    </macros>
    <expand macro="python_requirements">
        <requirement type="package" version="2.2.5">viennarna</requirement>
        <requirement type="package" version="2.1.6">rnashapes</requirement>
    </expand>
    <expand macro="macro_stdio"/>
    <version_command>echo "@VERSION@"</version_command>
    <command>
        <![CDATA[
        python "$eden_converter_script" '$inputs'
        ]]>
    </command>
    <configfiles>
        <inputs name="inputs" />
        <configfile name="eden_converter_script">
            <![CDATA[
import sys
import json
import networkx
from eden.converter.fasta import fasta_to_sequence
from eden.converter.rna.rnashapes import rnashapes_to_eden
from eden.converter.rna.rnafold import rnafold_to_eden
from eden.converter.graph.node_link_data import eden_to_node_link_data
#*from eden.converter.graph.node_link_data import eden_to_node_link_file*#

input_json_path = sys.argv[1]
params = json.load(open(input_json_path, "r"))

sequence_iterable = fasta_to_sequence("$infile")

if "$converter_options.selected_converter" == "rnafold_to_eden":
    graph_list = rnafold_to_eden(sequence_iterable)
elif "$converter_options.selected_converter" == "rnashapes_to_eden":
    params["converter_options"].pop('selected_converter')
    sub_params = params["converter_options"]["options"]
    graph_list = rnashapes_to_eden(sequence_iterable, **sub_params )

json_graph_list = eden_to_node_link_data(graph_list)

#*TODO: replace with eden_to_node_link_file(graph_list, fname)*#
with open("$outfile", 'w+') as out_file:
    for json_graph in json_graph_list:
        out_file.write(json_graph + '\n')
            ]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="infile" type="data" format="fasta" label="Fasta file" help="File including lines with FASTA format."/>
        <conditional name="converter_options">
            <param name="selected_converter" type="select" label="Folding algorithm">
                <option value="rnafold_to_eden">RNAfold</option>
                <option value="rnashapes_to_eden">RNAshapes</option>
            </param>
            <when value="rnafold_to_eden">
            </when>
            <when value="rnashapes_to_eden">
                <section name="options" title="Advanced Options" expanded="False">
                    <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 )"/>
                    <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 )"/>
                    <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 )"/>
                    <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 )"/>
                </section>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="json" name="outfile"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="RF01704.fasta" ftype="fasta"/>
            <param name="selected_converter" value="rnafold_to_eden"/>
            <output name="outfile" file="converter_result01.json"/>
        </test>
        <test>
            <param name="infile" value="RF01704.fasta" ftype="fasta"/>
            <param name="selected_converter" value="rnashapes_to_eden"/>
            <param name="shape_type" value="2" />
            <param name="energy_range" value="4" />
            <param name="max_num" value="3" />
            <param name="split_components" value="true" />
            <output name="outfile" file="converter_result02.json"/>
        </test>
    </tests>
    <help>
        <![CDATA[
        **What it does**
        
        This tool transforms fasta sequences to graphs that encode secondary structure information.

        Users can choose between two RNA folding algorithms:

        1. RNAfold to predict the Minimum Free Energy (mfe) structure.

        2. RNAshapes to predict a specified number of shapes with the highest occurrence probability.

        ]]>
    </help>
    <expand macro="eden_citation"/>
</tool>