comparison macros.xml @ 2:c3a4fb832c18 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73

1:9cd90b2f08f7

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

    <token name="@STACKS_VERSION@">2.2</token>
    <token name="@WRAPPER_VERSION@">1</token>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error in Stacks execution" />
        </stdio>

        <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">
            <filter>add_log</filter>
        </data>
    </xml>

    <!-- fastq input -->
    <xml name="fastq_input_macro" token_fastq_optional="false">
        <conditional name="input_type">
            <param name="input_type_selector" type="select" label="Short read data from individuals" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks">
                <option value="manual" selected="true">single end or forward reads</option>

            </param>
            <when value="manual">
                <param name="samples" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/>
            </when>
            <when value="list">
                <param name="samples" argument="-f" type="data_collection" collection_type="list,list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/>
            </when>
        </conditional>
    </xml>
    <!-- requires a variable $read_direction=None|"forward"|"reverse" to be set 
         appends noting/.1/.2 to the link name for accessing the fastq data
         sets variables $name and $data_path-->
    <token name="@FASTQ_INPUT@"><![CDATA[
    #set $name = $clean_ext($sample.name)
    #set $data_path = "stacks_inputs/" + $name
    #if $sample.is_collection:
        #set $sample=$sample[$read_direction]
    #end if
    #if $read_direction == "forward":
        #set $data_path =  $data_path + ".1"
    #elif $read_direction == "reverse":
        #set $data_path =  $data_path + ".2"
    #end if
    #if $sample.is_of_type('fastqsanger')
        #set $data_path =  $data_path + ".fq"
        #set inputype = "fastq"
    #else if $sample.is_of_type('fastqsanger.gz')
        #set $data_path = $data_path + ".fq.gz"
        #set inputype = "gzfastq"
    #else if $sample.is_of_type('fasta')
        #set $data_path = $data_path + ".fa"
        #set inputype = "fasta"
    #else
        #set $data_path = $data_path + ".fa.gz"
        #set inputype = "gzfasta"
    #end if
    ln -s '$sample' '${data_path}' &&
    ]]></token>

    <!-- macro and token for BAM input-->
    <xml name="bam_input_macro">
        <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" />

            #set bamlist += " -B 'bam_inputs/"+$filename+"'"
        #end if
    #end for
    ]]></token>

    <xml name="discover_faqgz_output_macro" token_pattern="" token_dir="">
        <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/>
        <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/" />
        <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/" />
    </xml>
    <xml name="discover_faq_output_macro" token_pattern="" token_dir="">
        <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/" />
        <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/" />
    </xml>
    <token name="@CLEAN_EXT@">
        <![CDATA[
        #from os.path import splitext
        #import re
        #def clean_ext($identifier)

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

    <xml name="barcode_encoding_pair">
        <expand macro="barcode_encoding_single">    
            <option value="--null_index">barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided)</option>
            <option value="--inline_inline">barcode is inline with sequence, occurs on single and paired-end read</option>
            <option value="--index_index">barcode is provded in FASTQ header (Illumina i5 and i7 reads).</option>
            <option value="--inline_index">barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read)</option>
            <option value="--index_inline"></option>
        </expand>    
    </xml>
</macros>

2:c3a4fb832c18

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

    <token name="@STACKS_VERSION@">2.2</token>
    <token name="@WRAPPER_VERSION@">2</token>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error in Stacks execution" />
        </stdio>

        <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">
            <filter>add_log</filter>
        </data>
    </xml>


    <!-- fastq input -->
    <xml name="fastq_input_macro" token_fastq_optional="false">
        <conditional name="input_type">
            <param name="input_type_selector" type="select" label="Short read data from individuals" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks">
                <option value="manual" selected="true">single end or forward reads</option>

            </param>
            <when value="manual">
                <param name="samples" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/>
            </when>
            <when value="list">
                <param name="samples" argument="-f" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/>
            </when>
        </conditional>
    </xml>
    <!-- requires a variable $read_direction=None|"forward"|"reverse" to be set 
         appends noting/.1/.2 to the link name for accessing the fastq data
         sets variables $name and $data_path-->
    <token name="@FASTQ_INPUT@"><![CDATA[
    ## TODO should use sample.identidfier if possible (see corresp. preproc macro)
    #set $name = $clean_ext($sample.name)
    #set $data_path = "stacks_inputs/" + $name
    #if $sample.is_collection:
        #set $cur_sample=$sample[$read_direction]
    #else:
        #set $cur_sample=$sample
    #end if
    #if $read_direction == "forward":
        #set $data_path =  $data_path + ".1"
    #elif $read_direction == "reverse":
        #set $data_path =  $data_path + ".2"
    #end if
    #if $cur_sample.is_of_type('fastqsanger')
        #set $data_path =  $data_path + ".fq"
        #set inputype = "fastq"
    #else if $cur_sample.is_of_type('fastqsanger.gz')
        #set $data_path = $data_path + ".fq.gz"
        #set inputype = "gzfastq"
    #else if $cur_sample.is_of_type('fasta')
        #set $data_path = $data_path + ".fa"
        #set inputype = "fasta"
    #else
        #set $data_path = $data_path + ".fa.gz"
        #set inputype = "gzfasta"
    #end if
    ln -s '$cur_sample' '${data_path}' &&
    ]]></token>

    <!-- macro and token for BAM input-->
    <xml name="bam_input_macro">
        <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" />

            #set bamlist += " -B 'bam_inputs/"+$filename+"'"
        #end if
    #end for
    ]]></token>

    <token name="@CLEAN_EXT@">
        <![CDATA[
        #from os.path import splitext
        #import re
        #def clean_ext($identifier)

    </xml>
    <xml name="variant_calling_options_g">
        <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>
        <yield/>
    </xml>

    <xml name="barcode_encoding_pair" token_type="">
        <expand macro="barcode_encoding_single" type="@TYPE@">    
            <option value="--null_index">@TYPE@ is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided) (--null_index)</option>
            <option value="--inline_inline">@TYPE@ is inline with sequence, occurs on single and paired-end read (--inline_inline)</option>
            <option value="--index_index">@TYPE@ is provded in FASTQ header (Illumina i5 and i7 reads) (--index_index)</option>
            <option value="--inline_index">@TYPE@ is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read) (--inline_index)</option>
            <option value="--index_inline">@TYPE@ occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data) (--index_inline)</option>
        </expand>    
    </xml>
</macros>