comparison dada2_primercheck.xml @ 2:c05ea8df8ad2 draft default tip

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

1:c7d45735c578

df <- NULL;
#for $i, $read in enumerate($paired_cond.reads):
    #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
    #if $paired_cond.paired_select == "single"
        #set fwd_reads = $read
    #elif $paired_cond.paired_select == "separate"
        #set fwd_reads = $read
        #set rev_reads = $paired_cond.sdaer[i]
    #else
        #set fwd_reads = $read.forward
        #set rev_reads = $read.reverse
    #end if
    df <- rbind(df, c('$elid', 'FWD', 'FWD', sapply(FWD.orients, primerHits, fn = '$fwd_reads')))
    df <- rbind(df, c('$elid', 'REV', 'FWD', sapply(REV.orients, primerHits, fn = '$fwd_reads')))
    #if $paired_cond.paired_select != "single"
        #if $paired_cond.paired_select == "separate"
            #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.sdaer[i].element_identifier))
        #end if
        df <- rbind(df, c('$elid', 'FWD', 'REV', sapply(FWD.orients, primerHits, fn = '$rev_reads')))
        df <- rbind(df, c('$elid', 'REV', 'REV', sapply(REV.orients, primerHits, fn = '$rev_reads')))
    #end if
#end for
colnames(df) <- c('Sample', 'Primer', 'ReadDir', 'Sequence', 'Complement', 'Reverse', 'RevComp')

                    <has_n_lines n="9"/>
                    <has_n_columns n="7"/>
                </assert_contents>
            </output>
        </test>
        <!-- paired data in separate collection -->
        <test expect_num_outputs="1">
            <conditional name="paired_cond">
                <param name="paired_select" value="separate"/>
                <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
                <param name="sdaer" value="F3D0_S188_L001_R2_001.fastq.gz,F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
            </conditional>

            <param name="forward_primer" value="ACCTGCGGARGGATCA"/>
            <param name="reverse_primer" value="GAGATCCRTTGYTRAAAGTT"/>
            <output name="out">
                <assert_contents>
                    <has_n_lines n="9"/>
                    <has_n_columns n="7"/>
                </assert_contents>
            </output>
        </test>
        <!-- single end data -->
        <test expect_num_outputs="1">
            <conditional name="paired_cond">
                <param name="paired_select" value="single"/>
                <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>

2:c05ea8df8ad2

df <- NULL;
#for $i, $read in enumerate($paired_cond.reads):
    #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
    #if $paired_cond.paired_select == "single"
        #set fwd_reads = $read
    #else
        #set fwd_reads = $read.forward
        #set rev_reads = $read.reverse
    #end if
    df <- rbind(df, c('$elid', 'FWD', 'FWD', sapply(FWD.orients, primerHits, fn = '$fwd_reads')))
    df <- rbind(df, c('$elid', 'REV', 'FWD', sapply(REV.orients, primerHits, fn = '$fwd_reads')))
    #if $paired_cond.paired_select != "single"
        df <- rbind(df, c('$elid', 'FWD', 'REV', sapply(FWD.orients, primerHits, fn = '$rev_reads')))
        df <- rbind(df, c('$elid', 'REV', 'REV', sapply(REV.orients, primerHits, fn = '$rev_reads')))
    #end if
#end for
colnames(df) <- c('Sample', 'Primer', 'ReadDir', 'Sequence', 'Complement', 'Reverse', 'RevComp')

                    <has_n_lines n="9"/>
                    <has_n_columns n="7"/>
                </assert_contents>
            </output>
        </test>
        <!-- single end data -->
        <test expect_num_outputs="1">
            <conditional name="paired_cond">
                <param name="paired_select" value="single"/>
                <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>