comparison stacks_populations.xml @ 6:e2db212d64ad draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"

5:7b881f5f5ad5

<tool id="stacks2_populations" name="Stacks2: populations" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
    <description>Calculate population-level summary statistics</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

$populations_output.fasta_samples
$populations_output.vcf
$populations_output.genepop
$populations_output.structure
$populations_output.radpainter
##$populations_output.phase
##$populations_output.fastphase
$populations_output.plink
$populations_output.hzar
$populations_output.phylip
$populations_output.phylip_var
##$populations_output.phylip_var_all

            <param argument="--fasta-samples" truevalue="--fasta-samples" falsevalue="" type="boolean" checked="false" label="Output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format"/>
            <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)"/>
            <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format"/>
            <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format"/>
            <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="Output results in fineRADstructure/RADpainter format"/>
            <!--<param argument="\-\-phase" truevalue="\-\-phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format"/>-->
            <param argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format"/>
            <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format"/>
            <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format."/>
            <param argument="--phylip" truevalue="--phylip" falsevalue="" type="boolean" checked="false" label="Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction"/>
            <param argument="--phylip-var" truevalue="--phylip-var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation."/>
            <!--<param argument="\-\-phylip_var_all" truevalue="\-\-phylip-var-all" falsevalue="" type="boolean" checked="false" label="Include all sequence as well as variable sites in the phylip output encoded using IUPAC notation."/>-->

                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
               </collection>
            </param>
            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
            <param name="add_log" value="yes"/>
            <param name="advanced_options|log_fst_comp" value="yes"/>
            <param name="fstats_conditional|fstats" value="yes"/>
            <param name="populations_output|fasta_loci" value="yes"/>
            <param name="populations_output|fasta_samples" value="yes"/>
            <param name="populations_output|fasta_samples_raw" value="yes"/>
            <param name="populations_output|phylip" value="yes"/>
            <param name="populations_output|phylip_var" value="yes"/>
            <param name="populations_output|genepop" value="yes"/>
            <param name="populations_output|vcf" value="yes"/>
            <param name="populations_output|hzar" value="yes"/>
            <param name="populations_output|plink" value="yes"/>
            <param name="populations_output|structure" value="yes"/>
            <param name="populations_output|radpainter" value="yes"/>
            <param name="populations_output|treemix" value="yes"/>
            <param name="populations_output|gtf" value="yes"/>
            <assert_command>
                <has_text text="--log-fst-comp"/>
            </assert_command>
            <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
            <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>

6:e2db212d64ad

<tool id="stacks2_populations" name="Stacks2: populations" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Calculate population-level summary statistics</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

$populations_output.fasta_samples
$populations_output.vcf
$populations_output.genepop
$populations_output.structure
$populations_output.radpainter
$populations_output.plink
$populations_output.hzar
$populations_output.phylip
$populations_output.phylip_var
##$populations_output.phylip_var_all

            <param argument="--fasta-samples" truevalue="--fasta-samples" falsevalue="" type="boolean" checked="false" label="Output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format"/>
            <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)"/>
            <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format"/>
            <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format"/>
            <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="Output results in fineRADstructure/RADpainter format"/>
            <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format"/>
            <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format."/>
            <param argument="--phylip" truevalue="--phylip" falsevalue="" type="boolean" checked="false" label="Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction"/>
            <param argument="--phylip-var" truevalue="--phylip-var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation."/>
            <!--<param argument="\-\-phylip_var_all" truevalue="\-\-phylip-var-all" falsevalue="" type="boolean" checked="false" label="Include all sequence as well as variable sites in the phylip output encoded using IUPAC notation."/>-->

                    <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz"/>
               </collection>
            </param>
            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
            <param name="add_log" value="yes"/>
            <param name="advanced_options|log_fst_comp" value="true"/>
            <param name="fstats_conditional|fstats" value="yes"/>
            <param name="populations_output|fasta_loci" value="true"/>
            <param name="populations_output|fasta_samples" value="true"/>
            <param name="populations_output|fasta_samples_raw" value="true"/>
            <param name="populations_output|phylip" value="true"/>
            <param name="populations_output|phylip_var" value="true"/>
            <param name="populations_output|genepop" value="true"/>
            <param name="populations_output|vcf" value="true"/>
            <param name="populations_output|hzar" value="true"/>
            <param name="populations_output|plink" value="true"/>
            <param name="populations_output|structure" value="true"/>
            <param name="populations_output|radpainter" value="true"/>
            <param name="populations_output|treemix" value="true"/>
            <param name="populations_output|gtf" value="true"/>
            <assert_command>
                <has_text text="--log-fst-comp"/>
            </assert_command>
            <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
            <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>