comparison macros.xml @ 1:f4aab9196d1e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"

0:da351b9031de

            <yield/>
        </requirements>
    </xml>

    <token name="@STACKS_VERSION@">2.4</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>

        <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) 
         - se_option: wording for "single end" option (for tsv2bam this is the
              reverse reads for the others its the forward reads)
         - help: help text -->
    <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help="">
        <conditional name="input_type">

        <expand macro="snp_options">
            <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/>
        </expand>
    </xml>

	<!-- variant calling option for use in gstacks and denovomap 
         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>

1:f4aab9196d1e

            <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>

        <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)
         - se_option: wording for "single end" option (for tsv2bam this is the
              reverse reads for the others its the forward reads)
         - help: help text -->
    <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help="">
        <conditional name="input_type">

        <expand macro="snp_options">
            <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/>
        </expand>
    </xml>

	<!-- variant calling option for use in gstacks and denovomap
         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>