comparison macros.xml @ 2:bd5ff77e2036 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"

1:ca7aa77c7f57

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@STACKS_VERSION@">2.4</token>
    <token name="@WRAPPER_VERSION@">1</token>
    <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->
    <token name="@PROFILE@">18.01</token>

    <xml name="citation">
        <citations>

    </xml>

    <!-- log file handling -->
    <token name="@TEE_APPEND_LOG@"><![CDATA[
        #if $output_log
            2>> '$output_log' &&
        #end if
    ]]></token>
    <token name="@CAT_LOG_TO_STDERR@"><![CDATA[
        #if $output_log
            cat '$output_log' 2>&1
        #end if
    ]]></token>
    <xml name="in_log">
        <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset" />
    </xml>
    <xml name="out_log">
        <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">
            <filter>add_log</filter>
        </data>
    </xml>

    <!-- inputs from previous pipeline steps -->
    <xml name="input_stacks_macro">
        <param name="input_stacks" format="tabular,txt" type="data_collection" collection_type="list" label="Loci and polymorphism" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks" />
    </xml>
    <xml name="input_cat_macro">
        <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog of loci" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" />
    </xml>
    <xml name="input_matches_macro">
        <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks" />
    </xml>
    <xml name="bam_input_macro">
        <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference" />
    </xml>
    <xml name="input_aln_macro">
        <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" />
    </xml>

    <!-- code for creating links to the data sets from previous pipeline steps
         - stacks (i.e ustacks outputs POP.tags.tsv, POP.alleles.tsv, POP.snps.tsv)
             also stores sample names in list (samples)

            <param name="input_type_select" type="select" label="Single-end or paired-end reads">
                <option value="single" selected="True">Single-end files</option>
                <option value="paired">Paired-end files</option>
            </param>
            <when value="single">
                <param name="fqinputs" argument="-f" type="data" format="fastqsanger,fastqsanger.gz" multiple="@MULTIPLE@" label="Singles-end reads" />
                <param name="barcode_encoding" type="select" label="Barcode location">
                    <expand macro="barcode_encoding_single" type="Barcode" />
                </param>
            </when>
            <when value="paired">
                <param name="fqinputs" type="data_collection" collection_type="@LISTTYPE@" label="Paired-end reads" format="fastqsanger,fastqsanger.gz"/>
                <param name="barcode_encoding" type="select" label="Barcode location">
                    <expand macro="barcode_encoding_pair" type="Barcode" />
                </param>
            </when>
        </conditional>
        <yield/>
    </xml>

    <xml name="fastq_input_bc_file" token_multiple="false" token_listtype="paired">
        <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@">
            <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" />
        </expand>
    </xml>

    <!-- fastq input (used in denovomap, tsv2bam, ustacks)
         - fastq_optional: makes fastq input optional (true/false)

    <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) -->
    <!-- TODO tags, snps, and alleles could go to sub collections; same for other tools -->
    <xml name="ustacks_outputs_macro" token_tooladd="">
        <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci and polymorphism">
            <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
        </collection>
    </xml>
    <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv -->
    <xml name="cstacks_outputs_macro" token_tooladd="">
        <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog of loci">
            <discover_datasets pattern="(?P&lt;name&gt;catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" />
        </collection>
    </xml>
    <!-- sstacks outputs collection containing SAMPLE.matches.tsv -->
    <xml name="sstacks_outputs_macro" token_tooladd="">
        <collection name="matches" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog">
            <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
        </collection>
    </xml>
    <!-- tsv2bam outputs collection containing SAMPLE.matches.bam -->
    <xml name="tsv2bam_outputs_macro" token_tooladd="">
        <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog (bam)">
            <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.bam$" ext="bam" directory="stacks_outputs" />
        </collection>
    </xml>
    <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz
         + optional output alignments.bam (if no popmap is given) and POP.alns.bam otherwise-->
    <xml name="gstacks_outputs_full_macro" token_tooladd="">
        <expand macro="gstacks_outputs_macro"/>
        <data format="txt" name="distribs" label="${tool.name} on ${on_string} log.distribs" from_work_dir="stacks_outputs/gstacks.log.distribs">
            <filter>add_log_distribs</filter>
        </data>
        <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments">
            <discover_datasets pattern="(?P&lt;name&gt;.*).alns.bam$" ext="bam" directory="stacks_outputs" />
            <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap!=None</filter>
        </collection>
        <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam">
            <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap==None</filter>
        </data>
    </xml>
    <xml name="gstacks_outputs_macro" token_tooladd="">
        <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites">
            <discover_datasets pattern="(?P&lt;name&gt;catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs" />
        </collection>
    </xml>

    <!-- default output of populations -->
    <xml name="populations_output_light" token_tooladd="">
        <data format="tabular" name="out_haplotypes" label="${tool.name} @TOOLADD@ on ${on_string} Raw Genotypes/Haplotypes" from_work_dir="stacks_outputs/populations.haplotypes.tsv" />
        <data format="tabular" name="out_hapstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level haplotype summary statistics" from_work_dir="stacks_outputs/populations.hapstats.tsv" />
        <data format="txt" name="out_populations_log_distribs" label="${tool.name} @TOOLADD@ on ${on_string} Populations log distributions" from_work_dir="stacks_outputs/populations.log.distribs" />
        <data format="tabular" name="out_sumstats_sum" label="${tool.name} @TOOLADD@ on ${on_string} Summary of Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats_summary.tsv" />
        <data format="tabular" name="out_sumstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats.tsv" />
        <data format="tabular" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.markers.tsv" />
    </xml>

    <xml name="populations_output_full">
        <expand macro="populations_output_light"/>

        <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv-->
        <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv">
            <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
        </data>

        <!-- treemix populations.treemix -->
        <data format="tabular" name="out_treemix" label="${tool.name} on ${on_string} Treemix format" from_work_dir="stacks_outputs/populations.treemix">
            <filter>populations_output['treemix']</filter>
        </data>
    </xml>

    <xml name="snp_options_alpha">
        <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
            <option value="0.1">0.1</option>

            <when value="snp">
                <expand macro="snp_options_alpha"/>
            </when>
            <when value="bounded">
                <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="Lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
                <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="Upper bound for epsilon, the error rate" help="between 0 and 1.0" />
                <expand macro="snp_options_alpha"/>
            </when>
            <when value="fixed">
                <yield/>
            </when>

         default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap)
         otherwise no default is is available and gstacks will output and error
         "Error: No value was provided for \-\-var-alpha and there is no default for this model)"
	-->
    <xml name="variant_calling_options_vg" token_varalpha_default="">
        <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available." />
        <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" />
    </xml>

    <xml name="barcode_encoding_single" token_type="">
        <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option>
        <option value="--index_null">@TYPE@ is provded in FASTQ header (Illumina i5 or i7 read) (--index_null)</option>

2:bd5ff77e2036

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
            <requirement type="package" version="3.7">python</requirement>
            <requirement type="package" version="4.6.0">findutils</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@STACKS_VERSION@">2.53</token>
    <token name="@WRAPPER_VERSION@">0</token>
    <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->
    <token name="@PROFILE@">18.01</token>

    <xml name="citation">
        <citations>

    </xml>

    <!-- log file handling -->
    <token name="@TEE_APPEND_LOG@"><![CDATA[
        #if $output_log
            2> '$output_log'
        #end if
    ]]></token>
    <xml name="in_log">
        <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset"/>
    </xml>
    <xml name="out_log">
        <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">
            <filter>add_log</filter>
        </data>
    </xml>

    <!-- inputs from previous pipeline steps -->
    <xml name="input_stacks_macro">
        <param name="input_stacks" format="tabular,txt" type="data_collection" collection_type="list" label="Loci and polymorphism" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks"/>
    </xml>
    <xml name="input_cat_macro">
        <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog of loci" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks"/>
    </xml>
    <xml name="input_matches_macro">
        <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks"/>
    </xml>
    <xml name="bam_input_macro">
        <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference"/>
    </xml>
    <xml name="input_aln_macro">
        <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P"/>
    </xml>

    <!-- code for creating links to the data sets from previous pipeline steps
         - stacks (i.e ustacks outputs POP.tags.tsv, POP.alleles.tsv, POP.snps.tsv)
             also stores sample names in list (samples)

            <param name="input_type_select" type="select" label="Single-end or paired-end reads">
                <option value="single" selected="True">Single-end files</option>
                <option value="paired">Paired-end files</option>
            </param>
            <when value="single">
                <param name="fqinputs" argument="-f" type="data" format="fastqsanger,fastqsanger.gz" multiple="@MULTIPLE@" label="Singles-end reads"/>
                <param name="barcode_encoding" type="select" label="Barcode location">
                    <expand macro="barcode_encoding_single" type="Barcode"/>
                </param>
            </when>
            <when value="paired">
                <param name="fqinputs" type="data_collection" collection_type="@LISTTYPE@" label="Paired-end reads" format="fastqsanger,fastqsanger.gz"/>
                <param name="barcode_encoding" type="select" label="Barcode location">
                    <expand macro="barcode_encoding_pair" type="Barcode"/>
                </param>
            </when>
        </conditional>
        <yield/>
    </xml>

    <xml name="fastq_input_bc_file" token_multiple="false" token_listtype="paired">
        <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@">
            <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file"/>
        </expand>
    </xml>

    <!-- fastq input (used in denovomap, tsv2bam, ustacks)
         - fastq_optional: makes fastq input optional (true/false)

    <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) -->
    <!-- TODO tags, snps, and alleles could go to sub collections; same for other tools -->
    <xml name="ustacks_outputs_macro" token_tooladd="">
        <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci and polymorphism">
            <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs"/>
            <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs"/>
            <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs"/>
        </collection>
    </xml>
    <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv -->
    <xml name="cstacks_outputs_macro" token_tooladd="">
        <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog of loci">
            <discover_datasets pattern="(?P&lt;name&gt;catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs"/>
        </collection>
    </xml>
    <!-- sstacks outputs collection containing SAMPLE.matches.tsv -->
    <xml name="sstacks_outputs_macro" token_tooladd="">
        <collection name="matches" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog">
            <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs"/>
        </collection>
    </xml>
    <!-- tsv2bam outputs collection containing SAMPLE.matches.bam -->
    <xml name="tsv2bam_outputs_macro" token_tooladd="">
        <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog (bam)">
            <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.bam$" ext="bam" directory="stacks_outputs"/>
        </collection>
    </xml>
    <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz
         + optional output alignments.bam (if no popmap is given) and POP.alns.bam otherwise-->
    <xml name="gstacks_outputs_full_macro" token_tooladd="">
        <expand macro="gstacks_outputs_macro"/>
        <data format="txt" name="distribs" label="${tool.name} on ${on_string} log.distribs" from_work_dir="stacks_outputs/gstacks.log.distribs">
            <filter>add_log_distribs</filter>
        </data>
        <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments">
            <discover_datasets pattern="(?P&lt;name&gt;.*).alns.bam$" ext="bam" directory="stacks_outputs"/>
            <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap!=None</filter>
        </collection>
        <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam">
            <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap==None</filter>
        </data>
    </xml>
    <xml name="gstacks_outputs_macro" token_tooladd="">
        <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites">
            <discover_datasets pattern="(?P&lt;name&gt;catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs"/>
            <discover_datasets pattern="(?P&lt;name&gt;catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs"/>
        </collection>
    </xml>

    <!-- default output of populations -->
    <xml name="populations_output_light" token_tooladd="">
        <data format="tabular" name="out_haplotypes" label="${tool.name} @TOOLADD@ on ${on_string} Raw Genotypes/Haplotypes" from_work_dir="stacks_outputs/populations.haplotypes.tsv"/>
        <data format="tabular" name="out_hapstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level haplotype summary statistics" from_work_dir="stacks_outputs/populations.hapstats.tsv"/>
        <data format="txt" name="out_populations_log_distribs" label="${tool.name} @TOOLADD@ on ${on_string} Populations log distributions" from_work_dir="stacks_outputs/populations.log.distribs"/>
        <data format="tabular" name="out_sumstats_sum" label="${tool.name} @TOOLADD@ on ${on_string} Summary of Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats_summary.tsv"/>
        <data format="tabular" name="out_sumstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats.tsv"/>
    </xml>

    <xml name="populations_output_full">
        <expand macro="populations_output_light"/>

        <data format="txt" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.sql.tsv">
            <filter>genetic_map_options['map_type'] and genetic_map_options['map_format']</filter>
        </data>

        <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv-->
        <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv">
            <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
        </data>

        <!-- treemix populations.treemix -->
        <data format="tabular" name="out_treemix" label="${tool.name} on ${on_string} Treemix format" from_work_dir="stacks_outputs/populations.treemix">
            <filter>populations_output['treemix']</filter>
        </data>
    </xml>

    <!-- fastq output for kmer/clone-filter -->
    <xml name="fastq_output_filter">
        <data name="clean" format_source="fqinputs" label="${tool.name} on ${on_string}">
            <filter>input_type['input_type_select'] == 'single'</filter>
            <yield/>
        </data>
        <collection name="clean_pair" type="paired" format_source="fqinputs" label="${tool.name} on ${on_string}">
            <filter>input_type['input_type_select'] == 'paired'</filter>
            <yield/>
        </collection>
        <data name="discarded" format_source="fqinputs" label="${tool.name} on ${on_string}: discarded reads">
            <filter>capture and input_type['input_type_select'] == 'single'</filter>
            <yield/>
        </data>
        <collection name="discarded_pair" format_source="fqinputs" type="paired" label="${tool.name} on ${on_string}: discarded reads">
            <filter>capture and input_type['input_type_select'] == 'paired'</filter>
            <yield/>
        </collection>
    </xml>

    <xml name="snp_options_alpha">
        <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
            <option value="0.1">0.1</option>

            <when value="snp">
                <expand macro="snp_options_alpha"/>
            </when>
            <when value="bounded">
                <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="Lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
                <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="Upper bound for epsilon, the error rate" help="between 0 and 1.0"/>
                <expand macro="snp_options_alpha"/>
            </when>
            <when value="fixed">
                <yield/>
            </when>

         default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap)
         otherwise no default is is available and gstacks will output and error
         "Error: No value was provided for \-\-var-alpha and there is no default for this model)"
	-->
    <xml name="variant_calling_options_vg" token_varalpha_default="">
        <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available."/>
        <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes"/>
    </xml>

    <xml name="barcode_encoding_single" token_type="">
        <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option>
        <option value="--index_null">@TYPE@ is provded in FASTQ header (Illumina i5 or i7 read) (--index_null)</option>