comparison dada2_plotComplexity.xml @ 11:224abe7c80ed draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 commit f65944aa0547c2fbe4b746cf443c85b2a76e9a48

10:6f06d501b7e6

        ln -s '$batch_cond.paired_cond.reads' forward/'$elid' &&
    #else
        ln -s '$batch_cond.paired_cond.reads.forward' forward/'$elid' &&
        ln -s '$batch_cond.paired_cond.reads.reverse' reverse/'$elid' &&
    #end if
    #if $batch_cond.paired_cond.paired_select == "separate"
        ln -s '$batch_cond.paired_cond.sdaer' reverse/'$elid' &&
    #end if
#else
    #for $read in $batch_cond.paired_cond.reads:
        #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
        #if $batch_cond.paired_cond.paired_select != "paired"
            ln -s '$read' forward/'$elid' &&
        #else
            ln -s '$read.forward' forward/'$elid' &&
            ln -s '$read.reverse' reverse/'$elid' &&
        #end if
    #end for
    #if $batch_cond.paired_cond.paired_select == "separate"
        #for $read in $batch_cond.paired_cond.sdaer:
            #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
            ln -s '$read' reverse/'$elid' &&
        #end for
    #end if
#end if

    Rscript --slave '$dada2_script'
    ]]></command>
    <configfiles>

            </param>
            <param name="batch_cond|aggregate" value="FALSE"/>
            <output name="output_fwd" value="complexity_fwd.pdf" ftype="pdf" compare="sim_size" delta="200"/>
            <output name="output_rev" value="complexity_rev.pdf" ftype="pdf" compare="sim_size" delta="200"/>
        </test>
        <!-- paired-separate joint, no-aggregate (sim_size because element ids differ) -->
        <test expect_num_outputs="2">
            <param name="batch_cond|batch_select" value="joint"/>
            <param name="batch_cond|paired_cond|paired_select" value="separate"/>
            <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz,F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="batch_cond|aggregate" value="FALSE"/>
            <output name="output_fwd" value="complexity_fwd.pdf" ftype="pdf" compare="sim_size" delta="200"/>
            <output name="output_rev" value="complexity_rev.pdf" ftype="pdf" compare="sim_size" delta="200"/>
        </test>
        <!-- single, non-batch, aggregate, small sample -->
        <test expect_num_outputs="1">
            <param name="batch_cond|batch_select" value="joint"/>
            <param name="batch_cond|paired_cond|paired_select" value="single"/>
            <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>

                <collection type="paired">
                    <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
                    <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
                </collection>
            </param>
            <output name="output_fwd" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
            <output name="output_rev" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
        </test>
        <!-- paired-separate batch  (sim_size because element ids differ)-->
        <test expect_num_outputs="2">
            <param name="batch_cond|batch_select" value="batch"/>
            <param name="batch_cond|paired_cond|paired_select" value="separate"/>
            <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
            <output name="output_fwd" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
            <output name="output_rev" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
        </test>
        <!-- single, batch -->
        <test expect_num_outputs="1">

11:224abe7c80ed

        ln -s '$batch_cond.paired_cond.reads' forward/'$elid' &&
    #else
        ln -s '$batch_cond.paired_cond.reads.forward' forward/'$elid' &&
        ln -s '$batch_cond.paired_cond.reads.reverse' reverse/'$elid' &&
    #end if
#else
    #for $read in $batch_cond.paired_cond.reads:
        #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
        #if $batch_cond.paired_cond.paired_select != "paired"
            ln -s '$read' forward/'$elid' &&
        #else
            ln -s '$read.forward' forward/'$elid' &&
            ln -s '$read.reverse' reverse/'$elid' &&
        #end if
    #end for
#end if

    Rscript --slave '$dada2_script'
    ]]></command>
    <configfiles>

            </param>
            <param name="batch_cond|aggregate" value="FALSE"/>
            <output name="output_fwd" value="complexity_fwd.pdf" ftype="pdf" compare="sim_size" delta="200"/>
            <output name="output_rev" value="complexity_rev.pdf" ftype="pdf" compare="sim_size" delta="200"/>
        </test>
        <!-- single, non-batch, aggregate, small sample -->
        <test expect_num_outputs="1">
            <param name="batch_cond|batch_select" value="joint"/>
            <param name="batch_cond|paired_cond|paired_select" value="single"/>
            <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>

                <collection type="paired">
                    <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
                    <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
                </collection>
            </param>
            <output name="output_fwd" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
            <output name="output_rev" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
        </test>
        <!-- single, batch -->
        <test expect_num_outputs="1">