comparison rnafold.xml @ 8:bdb786715d28 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29

7:86f517dcfdfb

<tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.3">
    <description>Calculate minimum free energy secondary structures and partition function of RNAs</description>
    <macros>
        <token name="@EXECUTABLE@">RNAfold</token>
        <import>macros.xml</import>
    </macros>

    -T $temperature
    --dangles=$dangling
    #if $layout_type ==0
        --layout-type=$general_options.layout_type
    #end if
    #if $mea:
        --MEA=$mea
    #end if
    #if $pf
        $pf
        #if $pfscale:
            --pfScale=$pfscale
        #end if
    #end if
    $advancedOptions.noconversion
    $advancedOptions.gquad
    $advancedOptions.nolp
    $advancedOptions.nops
    $advancedOptions.nogu

    #if str($input_source.select_fasta) == "false"
        "input.fasta"
    #else
        "${input_source.fasta_input}"
    #end if
    > '$tabular_file'
]]>
    </command>

    <inputs>
        <conditional name="input_source">

        </param>
        <param name="layout_type" type="select" label="Layout algorithm" argument="--layout_type" >
            <option value="1" selected="true">Default: Naview layout</option>
            <option value="0">Simple radial layout</option>
        </param>
        <param argument="--MEA" name="mea" type="float" value="1.0" optional="true" label="Gamma Value" help="Used for the calculation of the Maximum Expected accuracy"/>
        <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
        <param name="pfscale" type="float" value="1.07" optional="true" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/>
        <section name="advancedOptions" title="Advanced options">
            <param name="nops" type="boolean" truevalue="--noPS" falsevalue="" checked="false" label="Do not produce postscript drawing of the mfe structure (reduces run-time)" help="(--noPS)"/>
            <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
            <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
            <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/>

                help="When sequence IDs are automatically generated, they receive an increasing number, usually starting with 1. Using this parameter, the first number can be specified to the users requirements. Note: negative numbers are not allowed. Note: Setting this parameter implies continuous sequence IDs, i.e. it activates the −−continuous−ids flag.."
                argument="--id-start"/>
        </section>
    </inputs>
    <outputs>
        <data format="dbn" name="tabular_file"/>
        <collection name="sequence_outputs" type="list" label="rna_eps outputs">
            <filter>advancedOptions['nops'] is False</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" />
        </collection>
        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
            <filter>measelect['pf'] is True</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="select_fasta" value="true" />
            <param name="fasta_input" value="rnafold_input1.fa"/>
            <output name="tabular_file" file="rnafold_result1.txt"/>
        </test>
        <test>
            <param name="select_fasta" value="true" />
            <param name="fasta_input" value="rnafold_input2.fa"/>
            <param name="temperature" value="75"/>
            <output name="tabular_file" file="rnafold_result2.txt"/>
        </test>
        <test>
            <param name="select_fasta" value="false" />
            <param name="input_sequence" value="TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA"/>
            <output name="tabular_file" file="rnafold_result3.txt"/>
        </test>
        <test>
            <param name="select_fasta" value="true" />
            <param name="fasta_input" value="sample_3.fa"/>
            <conditional name="shapeOption">
              <param name="shapeSelector" value="isUsed"/>
            </conditional>
            <param name="shapeFile" value="sample_3.react"/>
            <output name="tabular_file" file="sample_3_result.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[
**RNAfold**

8:bdb786715d28

<tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.4">
    <description>Calculate minimum free energy secondary structures and partition function of RNAs</description>
    <macros>
        <token name="@EXECUTABLE@">RNAfold</token>
        <import>macros.xml</import>
    </macros>

    -T $temperature
    --dangles=$dangling
    #if $layout_type ==0
        --layout-type=$general_options.layout_type
    #end if
    
	#if $mea:
        #if $meagamma:
            --MEA=$meagamma
        #else
            --MEA
        #end if	 
    #end if
  
    #if $pf
        $pf
    #end if

    #if $pfscale:
        --pfScale=$pfscale
    #end if

    $advancedOptions.noconversion
    $advancedOptions.gquad
    $advancedOptions.nolp
    $advancedOptions.nops
    $advancedOptions.nogu

    #if str($input_source.select_fasta) == "false"
        "input.fasta"
    #else
        "${input_source.fasta_input}"
    #end if
    > '$dot_bracket_stdout'
]]>
    </command>

    <inputs>
        <conditional name="input_source">

        </param>
        <param name="layout_type" type="select" label="Layout algorithm" argument="--layout_type" >
            <option value="1" selected="true">Default: Naview layout</option>
            <option value="0">Simple radial layout</option>
        </param>

        <param name="mea" type="boolean" checked="false" falsevalue="" label="Calculate Maximum Expected accuracy" help="--MEA"/>
        <param name="meagamma" type="float"  optional="true" label="MEA-Gamma Value"/>

        <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
        <param name="pfscale" type="float" optional="true" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/>
        <section name="advancedOptions" title="Advanced options">
            <param name="nops" type="boolean" truevalue="--noPS" falsevalue="" checked="false" label="Do not produce postscript drawing of the mfe structure (reduces run-time)" help="(--noPS)"/>
            <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
            <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
            <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/>

                help="When sequence IDs are automatically generated, they receive an increasing number, usually starting with 1. Using this parameter, the first number can be specified to the users requirements. Note: negative numbers are not allowed. Note: Setting this parameter implies continuous sequence IDs, i.e. it activates the −−continuous−ids flag.."
                argument="--id-start"/>
        </section>
    </inputs>
    <outputs>
        <data format="dbn" name="dot_bracket_stdout"/>
        <collection name="structure_outputs" type="list" label="rna_strcuture_eps outputs">
            <filter>advancedOptions['nops'] is False</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" />
        </collection>
        <collection name="matrix_outputs" type="list" label="rna_matrix_eps outputs">
            <filter>pf is True</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="select_fasta" value="true" />
            <param name="fasta_input" value="rnafold_input1.fa"/>
            <output name="dot_bracket_stdout" file="rnafold_result1.txt"/>
        </test>
        
        <test>
            <param name="select_fasta" value="true" />
            <param name="mea" value="true" />
            <param name="fasta_input" value="rnafold_input1.fa"/>
            <output name="dot_bracket_stdout" file="rnafold_result1_mea.txt"/>
        </test>
        <test>
            <param name="select_fasta" value="true" />
            <param name="pf" value="true" />
            <param name="fasta_input" value="rnafold_input1.fa"/>
            <output name="dot_bracket_stdout" file="rnafold_result1_pf.txt"/>
            <output_collection name="structure_outputs" type="list">
                <element name="Anolis_caro_chrUn_GL343590.trna2_AlaAGC" file="Anolis_caro_chrUn_GL343590.trna2_AlaAGC_ss.ps"  compare="sim_size" />
                <element name="Anolis_caro_chrUn_GL343207.trna3_AlaAGC" file="Anolis_caro_chrUn_GL343207.trna3_AlaAGC_ss.ps"  compare="sim_size" />
            </output_collection>
            
            <output_collection name="matrix_outputs" type="list">
                <element name="Anolis_caro_chrUn_GL343590.trna2_AlaAGC" file="Anolis_caro_chrUn_GL343590.trna2_AlaAGC_dp.ps"  compare="sim_size" />
                <element name="Anolis_caro_chrUn_GL343207.trna3_AlaAGC" file="Anolis_caro_chrUn_GL343207.trna3_AlaAGC_dp.ps"  compare="sim_size" />
            </output_collection>
        </test>       
        <test>
            <param name="select_fasta" value="true" />
            <param name="fasta_input" value="rnafold_input2.fa"/>
            <param name="temperature" value="75"/>
            <output name="dot_bracket_stdout" file="rnafold_result2.txt"/>
        </test>
        <test>
            <param name="select_fasta" value="false" />
            <param name="input_sequence" value="TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA"/>
            <output name="dot_bracket_stdout" file="rnafold_result3.txt"/>
        </test>
        <test>
            <param name="select_fasta" value="true" />
            <param name="fasta_input" value="sample_3.fa"/>
            <conditional name="shapeOption">
              <param name="shapeSelector" value="isUsed"/>
            </conditional>
            <param name="shapeFile" value="sample_3.react"/>
            <output name="dot_bracket_stdout" file="sample_3_result.txt"/>
        </test>
    
    </tests>
    <help>
<![CDATA[
**RNAfold**