comparison stacks_procrad.xml @ 8:bec1f08cdfcc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e

7:f1f715f5d2f3

    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        #if $input_type.options_type_selector == "single":

            #if $input_type.input_single.is_of_type('fastqsanger'):
                #set $ext = ".fq"
                #set inputype = "fastq"
            #else:
                #set $ext = ".fq.gz"
                #set inputype = "gzfastq"
            #end if

            ln -s "$input_type.input_single" R1$ext &&
        #else

            #if $input_type.inputs_paired1.is_of_type('fastqsanger'):
                #set $ext = ".fq"
                #set inputype = "fastq"
            #else:
                #set $ext = ".fq.gz"
                #set inputype = "gzfastq"
            #end if

            ln -s "$input_type.inputs_paired1" R1$ext &&
            ln -s "$input_type.inputs_paired2" R2$ext &&
        #end if

        mkdir stacks_outputs

        &&

        process_radtags

            #if $input_type.options_type_selector == "single":
                -f R1$ext
            #else:
                -1 R1$ext
                -2 R2$ext
            #end if

            -i $inputype
            -b "$barcode"

            $input_type.barcode_encoding

            #if str( $options_enzyme.options_enzyme_selector ) == "1":
                -e $options_enzyme.enzyme
            #else:
                --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2
            #end if

            -y $outype

            $capture

            $options_advanced.retain_header

            #if str($options_advanced.truncate):
                -t $options_advanced.truncate
            #end if

            -w $options_advanced.sliding

            <param name="options_type_selector" type="select" label="Single-end or paired-end reads files">
                <option value="single" selected="True">Single-end files</option>
                <option value="paired">Paired-end files</option>
            </param>
            <when value="single">
                <param name="input_single" argument="-f" format="fastqsanger,fastq.gz" type="data" label="singles-end reads infile(s)" help="input files" />

                <param name="barcode_encoding" type="select" label="Barcode location">
                    <option value="--inline_null" selected="True">Barcode is inline with sequence</option>
                    <option value="--index_null">Barcode is provided in FASTQ header</option>
                </param>
            </when>
            <when value="paired">
                <param name="inputs_paired1" argument="-1" format="fastqsanger,fastq.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" />
                <param name="inputs_paired2" argument="-2" format="fastqsanger,fastq.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" />

                <param name="barcode_encoding" type="select" label="Barcode location">
                    <option value="--inline_null" selected="True">Barcode is inline with sequence, only on the single-end read (read 1)</option>
                    <option value="--index_null">Barcode is provided in FASTQ header, only on the single-end read (read 1)</option>
                    <option value="--inline_inline">Barcode is inline with sequence, on both single and paired-end read (read 1 and 2)</option>

            <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/>
            <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
            <param name="retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" />
        </section>

        <!-- Stacks can produce fastq.gz and fasta.gz output but we don't propose it as they are not very common datatypes in galaxy -->
        <param name="outype" argument="-y" type="select" label="Output format" help="output type, either 'fastq' or 'fasta'" >
            <option value="fastq" selected="True">fastq</option>
            <option value="fasta">fasta</option>
        </param>
    </inputs>

    <outputs>
        <data format="txt" name="output_log" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" from_work_dir="stacks_outputs/process_radtags.log" />

        <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}">
            <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
        </collection>
        <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}">
            <filter>input_type['options_type_selector'] == "paired"</filter>
            <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
        </collection>
        <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}">
            <filter>capture is True</filter>
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" />
        </collection>
    </outputs>

    <tests>

                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test>
            <param name="options_type_selector" value="paired"/>
            <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
            <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
            <param name="barcode" value="procrad/barcodes"/>
            <param name="options_enzyme_selector" value="1"/>

                <element name="R1">
                    <assert_contents>
                        <has_text text="lane1_fakedata0_11" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>

8:bec1f08cdfcc

    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[

        #if $input_type.options_type_selector == "single"

            #if $input_type.input_single.is_of_type('fastqsanger')
                #set $ext = ".fq"
                #set inputype = "fastq"
            #else
                #set $ext = ".fq.gz"
                #set inputype = "gzfastq"
            #end if

            ln -s '$input_type.input_single' R1$ext &&
        #else

            #if $input_type.inputs_paired1.is_of_type('fastqsanger')
                #set $ext = ".fq"
                #set inputype = "fastq"
            #else
                #set $ext = ".fq.gz"
                #set inputype = "gzfastq"
            #end if

            ln -s '$input_type.inputs_paired1' R1$ext &&
            ln -s '$input_type.inputs_paired2' R2$ext &&
        #end if

        mkdir stacks_outputs

        &&

        process_radtags

            #if $input_type.options_type_selector == "single"
                -f R1$ext
            #else
                -1 R1$ext
                -2 R2$ext
            #end if

            -i $inputype
            -b '$barcode'

            $input_type.barcode_encoding

            #if str( $options_enzyme.options_enzyme_selector ) == "1"
                -e $options_enzyme.enzyme
            #else
                --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2
            #end if

            #if str( $outype ) != "auto"
                -y $outype
            #end if

            $capture

            $options_advanced.retain_header

            #if str($options_advanced.truncate)
                -t $options_advanced.truncate
            #end if

            -w $options_advanced.sliding

            <param name="options_type_selector" type="select" label="Single-end or paired-end reads files">
                <option value="single" selected="True">Single-end files</option>
                <option value="paired">Paired-end files</option>
            </param>
            <when value="single">
                <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" />

                <param name="barcode_encoding" type="select" label="Barcode location">
                    <option value="--inline_null" selected="True">Barcode is inline with sequence</option>
                    <option value="--index_null">Barcode is provided in FASTQ header</option>
                </param>
            </when>
            <when value="paired">
                <param name="inputs_paired1" argument="-1" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" />
                <param name="inputs_paired2" argument="-2" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" />

                <param name="barcode_encoding" type="select" label="Barcode location">
                    <option value="--inline_null" selected="True">Barcode is inline with sequence, only on the single-end read (read 1)</option>
                    <option value="--index_null">Barcode is provided in FASTQ header, only on the single-end read (read 1)</option>
                    <option value="--inline_inline">Barcode is inline with sequence, on both single and paired-end read (read 1 and 2)</option>

            <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/>
            <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
            <param name="retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" />
        </section>

        <param name="outype" argument="-y" type="select" label="Output format" >
            <option value="auto" selected="True">Same as input</option>
            <option value="fastq">fastq</option>
            <option value="fasta">fasta</option>
            <option value="gzfastq">gzipped fastq</option>
        </param>
    </inputs>

    <outputs>
        <data format="txt" name="output_log" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" from_work_dir="stacks_outputs/process_radtags.log" />

        <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}">
            <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
        </collection>
        <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}">
            <filter>input_type['options_type_selector'] == "paired"</filter>
            <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
        </collection>
        <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}">
            <filter>capture is True</filter>
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" />
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.gz.discards$" ext="fastqsanger" directory="stacks_outputs" /> <!-- discards are never gzipped -->
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" />
        </collection>
    </outputs>

    <tests>

                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test>
            <param name="options_type_selector" value="single"/>
            <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/>
            <param name="barcode" value="procrad/barcodes"/>
            <param name="options_enzyme_selector" value="1"/>
            <param name="enzyme" value="ecoRI"/>
            <param name="discard" value="true"/>
            <param name="capture" value="true"/>
            <param name="outype" value="gzfastq"/>
            <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
            <output_collection name="demultiplexed">
                <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/>
            </output_collection>
            <output_collection name="discarded">
                <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/>
            </output_collection>
        </test>
        <test>
            <param name="options_type_selector" value="paired"/>
            <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
            <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
            <param name="barcode" value="procrad/barcodes"/>
            <param name="options_enzyme_selector" value="1"/>

                <element name="R1">
                    <assert_contents>
                        <has_text text="lane1_fakedata0_11" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test>
            <param name="options_type_selector" value="single"/>
            <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq.gzip"/>
            <param name="barcode" value="procrad/barcodes"/>
            <param name="options_enzyme_selector" value="1"/>
            <param name="enzyme" value="ecoRI"/>
            <param name="discard" value="true"/>
            <param name="capture" value="true"/>
            <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
            <output_collection name="demultiplexed">
                <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
            </output_collection>
            <output_collection name="discarded">
                <element name="R1">
                    <assert_contents>
                        <has_text text="lane1_fakedata0_11" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test>
            <param name="options_type_selector" value="single"/>
            <param name="input_single" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip"/>
            <param name="barcode" value="procrad/barcodes"/>
            <param name="options_enzyme_selector" value="1"/>
            <param name="enzyme" value="ecoRI"/>
            <param name="discard" value="true"/>
            <param name="capture" value="true"/>
            <param name="outype" value="gzfastq"/>
            <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
            <output_collection name="demultiplexed">
                <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq.gzip"/>
            </output_collection>
            <output_collection name="discarded">
                <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/>
            </output_collection>
        </test>
    </tests>