comparison macros.xml @ 5:3680074758c5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f

4:a70c766ce64f

            <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@STACKS_VERSION@">2.3c</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">

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

    </xml>
    <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="tabular,txt" 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)

        <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) -->
    <xml name="fastq_input" token_fastq_optional="false" token_help="">

        </data>
        <data format="tabular" name="out_plink_genotypes" label="${tool.name} on ${on_string} PLINK format (genotypes)" from_work_dir="stacks_outputs/populations.plink.ped">
            <filter>populations_output['plink']</filter>
        </data>

        <!--structure populations.structure-->
        <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure">
            <filter>populations_output['structure']</filter>
        </data>

        <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 -->
    <xml name="variant_calling_options_vg">
        <param argument="--var-alpha" name="var_alpha" type="float" value="0.01" min="0" label="Alpha threshold for discovering SNPs" />
        <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>

5:3680074758c5

            <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
            <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">

        #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>
    <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)

        <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) -->
    <xml name="fastq_input" token_fastq_optional="false" token_help="">

        </data>
        <data format="tabular" name="out_plink_genotypes" label="${tool.name} on ${on_string} PLINK format (genotypes)" from_work_dir="stacks_outputs/populations.plink.ped">
            <filter>populations_output['plink']</filter>
        </data>

		<!--structure populations.hzar-->
        <data format="tabular" name="out_hzar" label="${tool.name} on ${on_string} hzar format" from_work_dir="stacks_outputs/populations.hzar.csv">
            <filter>populations_output['hzar']</filter>
        </data>
        <!--structure populations.structure-->
        <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure">
            <filter>populations_output['structure']</filter>
        </data>

        <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>

    <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>