comparison allegro.xml @ 1:ef4a081bc97b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit bb83e01055cde8c766c630bec27afd3402ad6c88

0:8c29e3621475

<tool id="allegro" name="Allegro" version="@VER@.0" >
    <description>Linkage and Haplotype analysis</description>
    <macros>
        <token name="@VER@">2</token>
        <xml name="macro_inputs" >
            <param name="inp_ped" value="pedin.21" />
            <param name="inp_dat" value="datain.21" />
            <param name="inp_map" value="map.21" />
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="@VER@">allegro</requirement>
    </requirements>
    <version_command><![CDATA[
    allegro 2>&1 | head -1 | awk -F' ' '{print $2}'
    ]]>
    </version_command>

        #if $cond_haplotypes.opt_crossover
CROSSOVERRATE combined.out ${out_combined_cross}
        #end if
#elif $cond_haplotypes.opt_haplotypes.value == 'no'
    #if $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'defaults'
MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par ${opt_xlinked} het param.mpt ${out_fparam}

    #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'allele_sharing'
MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_linexp.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_scoring.value $cond_haplotypes.section_linkage.cond_linktype.extra_weighting.value param.mpt ${out_linexp}
 
    #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'classical'

    #elif $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'MAXSTEPLENGTH'
MAXSTEPLENGTH $cond_haplotypes.section_linkage.cond_steps.extra_maxstep
    #end if
#end if

#if $opt_xlinked.value == 'X'
SEXSPECIFIC on
#end if

ENTROPY ${opt_entropy}
NPLEXACTP ${opt_nplexactp}

PAIRWISEIBD $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_pairwise.extra_pairwise_type.value
#end if


#if $cond_sim.opt_sim.value == 'yes'
SIMULATE $cond_sim.extra_sim_dloc $cond_sim.extra_sim_npre $cond_sim.extra_sim_rep $cond_sim.extra_sim_err $cond_sim.extra_sim_yield $cond_sim.extra_sim_het
#end if

MAXMEMORY 102400
UNIT $opt_unit

                                <when value="yes" >
                                    <param name="extra_linkage_par_freq" type="float" value="0" min="0" max="1" label="Frequency" />
                                    <param name="extra_linkage_par_pen" type="text" value="p0/p1/p2" label="Penetrance" />
                                </when>
                            </conditional>
                            <param name="extra_linkage_par_het" type="float" value="" label="HET Frequency (leave blank for dynamic)" />
                        </when>
                    </conditional>

                    <conditional name="cond_steps" >
                        <param name="extra_steps_type" type="select" label="Step Type" >

                <option value="yes" >Yes</option>
                <option value="no" selected="true" >No</option>
            </param>
            <when value="no" />
            <when value="yes" >
                <param name="extra_sim_dloc" type="float" value="" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." />
                <param name="extra_sim_npre" type="integer" value="1" label="Number of prefiles to generate" />
                <param name="extra_sim_rep" type="integer" value="1" label="How many times to repeat family pattern" />
                <param name="extra_sim_err" type="float" value="0" min="0" label="Error Rate" />
                <param name="extra_sim_yield" type="float" value="1" label="Genotype Yield" />
                <param name="extra_sim_het" type="float" value="0" label="HET probability" />

        <param name="opt_sexspecific" type="boolean" truevalue="on" falsevalue="off" value="false" label="Use Sex-Specific Penetrances (specified in data file)" help="Note that you will need to include sex-specific penetrances in your data input file for this to work." />
        <param name="opt_unit" type="boolean" truevalue="centimorgan" falsevalue="recombination" value="false" label="Datafile uses centimorgan distances instead of recombination frequencies" />
    </inputs>

    <outputs>
        <data name="out_ihaplo" format="allegro_haplo" label="${tool.name} on ${on_string}: Haplotypes" />
        <data name="out_fparam" format="allegro_linkage" label="${tool.name} on ${on_string}: Linkage" />
        <data name="out_founder" format="allegro_descent" label="${tool.name} on ${on_string}: Descent" />
        <data name="out_linexp" format="txt" label="${tool.name} on ${on_string}: Linear Expression" />
        <data name="out_combined_cross" format="txt" label="${tool.name} on ${on_string}: Combined Crossovers" />
    </outputs>

    <tests>
        <test><!-- Default Haplotypes -->
            <expand macro="macro_inputs" />
            
            <param name="extra_linkage_type" value="classical" />
            <param name="extra_linkage_mptspt" value="mpt" />
            <param name="opt_haplotypes" value="yes" />

            <output name="out_ihaplo" >
                <assert_contents>
                    <has_text_matching expression="1\s+206003\s+111\s+112(\s+[012])+" />
                </assert_contents>
            </output>
        </test>
        <test><!-- Linkage with custom steps-->
            <expand macro="macro_inputs" />
            
            <param name="extra_linkage_type" value="classical" />
            <param name="extra_linkage_mptspt" value="mpt" />
            <param name="extra_linkage_mptspt" value="mpt" />
            <param name="extra_steps" value="3" />
            <param name="extra_maxstep" value="30" />


            <output name="out_fparam" >
                <assert_contents>
                    <has_text_matching expression="1(\s+[-0-9.]+){2}\s+rs2822572" />
                </assert_contents>
            </output>
        </test>
        <test><!-- Single-point linear expression test with power weights -->
            <expand macro="macro_inputs" />
            
            <param name="extra_linkage_type" value="allele_sharing" />
            <param name="extra_linkage_mptspt" value="spt" />
            <param name="extra_linkage_linexp" value="lin" />
            <param name="extra_linkage_scoring" value="homoz" />
            <param name="extra_weighting" value="power:50" />
                       
            <output name="out_fparam" >
                <assert_contents>
                    <has_text_matching expression='(\-\d+\.\d+\s+)+rs2822696' />
                </assert_contents>
            </output>

1:ef4a081bc97b

<tool id="allegro" name="Allegro" version="@TOOL_VERSION@.1" profile="21.05">
    <description>Linkage and Haplotype analysis</description>
    <macros>
        <token name="@TOOL_VERSION@">2</token>
        <xml name="macro_inputs" >
            <param name="inp_ped" value="pedin.21" />
            <param name="inp_dat" value="datain.21" />
            <param name="inp_map" value="map.21" />
        </xml>
    </macros>
    <xrefs>
        <xref type="bio.tools">allegro</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">allegro</requirement>
    </requirements>
    <version_command><![CDATA[
    allegro 2>&1 | head -1 | awk -F' ' '{print $2}'
    ]]>
    </version_command>

        #if $cond_haplotypes.opt_crossover
CROSSOVERRATE combined.out ${out_combined_cross}
        #end if
#elif $cond_haplotypes.opt_haplotypes.value == 'no'
    #if $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'defaults'
MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par $opt_xlinked het param.mpt ${out_fparam}

    #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'allele_sharing'
MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_linexp.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_scoring.value $cond_haplotypes.section_linkage.cond_linktype.extra_weighting.value param.mpt ${out_linexp}
 
    #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'classical'

    #elif $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'MAXSTEPLENGTH'
MAXSTEPLENGTH $cond_haplotypes.section_linkage.cond_steps.extra_maxstep
    #end if
#end if

#if $opt_sexspecific
SEXSPECIFIC on
#end if

ENTROPY ${opt_entropy}
NPLEXACTP ${opt_nplexactp}

PAIRWISEIBD $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_pairwise.extra_pairwise_type.value
#end if


#if $cond_sim.opt_sim.value == 'yes'
SIMULATE #slurp
#if $cond_sim.extra_sim_dloc != ""
dloc:$cond_sim.extra_sim_dloc #slurp
#end if
npre:$cond_sim.extra_sim_npre rep:$cond_sim.extra_sim_rep err:$cond_sim.extra_sim_err yield:$cond_sim.extra_sim_yield het:$cond_sim.extra_sim_het
#end if

MAXMEMORY 102400
UNIT $opt_unit

                                <when value="yes" >
                                    <param name="extra_linkage_par_freq" type="float" value="0" min="0" max="1" label="Frequency" />
                                    <param name="extra_linkage_par_pen" type="text" value="p0/p1/p2" label="Penetrance" />
                                </when>
                            </conditional>
                            <param name="extra_linkage_par_het" type="float" value="" optional="true" label="HET Frequency (leave blank for dynamic)" />
                        </when>
                    </conditional>

                    <conditional name="cond_steps" >
                        <param name="extra_steps_type" type="select" label="Step Type" >

                <option value="yes" >Yes</option>
                <option value="no" selected="true" >No</option>
            </param>
            <when value="no" />
            <when value="yes" >
                <param name="extra_sim_dloc" type="float" value="" optional="true" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." />
                <param name="extra_sim_npre" type="integer" value="1" label="Number of prefiles to generate" />
                <param name="extra_sim_rep" type="integer" value="1" label="How many times to repeat family pattern" />
                <param name="extra_sim_err" type="float" value="0" min="0" label="Error Rate" />
                <param name="extra_sim_yield" type="float" value="1" label="Genotype Yield" />
                <param name="extra_sim_het" type="float" value="0" label="HET probability" />

        <param name="opt_sexspecific" type="boolean" truevalue="on" falsevalue="off" value="false" label="Use Sex-Specific Penetrances (specified in data file)" help="Note that you will need to include sex-specific penetrances in your data input file for this to work." />
        <param name="opt_unit" type="boolean" truevalue="centimorgan" falsevalue="recombination" value="false" label="Datafile uses centimorgan distances instead of recombination frequencies" />
    </inputs>

    <outputs>
        <data name="out_ihaplo" format="allegro_ihaplo" label="${tool.name} on ${on_string}: Haplotypes" />
        <data name="out_fparam" format="allegro_fparam" label="${tool.name} on ${on_string}: Linkage" />
        <data name="out_founder" format="allegro_descent" label="${tool.name} on ${on_string}: Descent" />
        <data name="out_linexp" format="txt" label="${tool.name} on ${on_string}: Linear Expression" />
        <data name="out_combined_cross" format="txt" label="${tool.name} on ${on_string}: Combined Crossovers" />
    </outputs>

    <tests>
        <!-- Default Haplotypes -->
        <test>
            <expand macro="macro_inputs" />
            <conditional name="cond_haplotypes">
                <param name="opt_haplotypes" value="yes" />
            </conditional>
            <output name="out_ihaplo" >
                <assert_contents>
                    <has_text_matching expression="1\s+206003\s+111\s+112(\s+[012])+" />
                </assert_contents>
            </output>
        </test>
        <!-- Linkage with custom steps-->
        <test>
            <expand macro="macro_inputs" />
            <conditional name="cond_haplotypes">
                <section name="section_linkage">
                    <param name="extra_linkage_mptspt" value="mpt" />
                    <conditional name="cond_linktype" >
                        <param name="extra_linkage_type" value="classical" />
                    </conditional>
                    <conditional name="cond_steps" >
                        <param name="extra_steps" value="3" />
                    </conditional>
                </section>
            </conditional>
            <output name="out_fparam" >
                <assert_contents>
                    <has_text_matching expression="1(\s+[-0-9.]+){2}\s+rs2822572" />
                </assert_contents>
            </output>
        </test>
        <!-- Single-point linear expression test with power weights -->
        <test>
            <expand macro="macro_inputs" />
            <conditional name="cond_haplotypes">
                <section name="section_linkage">
                    <param name="extra_linkage_mptspt" value="spt" />
                    <conditional name="cond_linktype" >
                        <param name="extra_linkage_type" value="allele_sharing" />
                        <param name="extra_linkage_linexp" value="lin" />
                        <param name="extra_linkage_scoring" value="homoz" />
                        <param name="extra_weighting" value="power:0.5" />
                    </conditional>
                </section>
            </conditional>
            <output name="out_fparam" >
                <assert_contents>
                    <has_text_matching expression='(\-\d+\.\d+\s+)+rs2822696' />
                </assert_contents>
            </output>