comparison dada2_filterAndTrim.xml @ 8:e9d1e654cc9d draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty

7:146bee188fdf

fwd <- NULL
rev <- NULL
filt.fwd <- NULL
filt.rev <- NULL
#if $paired_cond.paired_select == "paired"
    fwd <- c(fwd, '$paired_cond.reads.forward')
    rev <- c(rev, '$paired_cond.reads.reverse')
    filt.fwd <- c(filt.fwd, '$paired_output.forward')
    filt.rev <- c(filt.rev, '$paired_output.reverse')
#else if $paired_cond.paired_select == "separate"
    fwd <- c(fwd, '$paired_cond.forward')
    rev <- c(rev, '$paired_cond.reverse')

    truncQ = truncQ, truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight, maxLen = maxLen,
    minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.phix = $rmPhiX, orient.fwd = '$orientFwd')

#if $paired_cond.paired_select == "separate":
    rownames(ftout) <- c( '$paired_cond.forward.element_identifier' )
#else:
    rownames(ftout) <- c( '$paired_cond.reads.element_identifier' )
#end if
write.table(ftout, "$outtab", quote=F, sep="\t", col.names=NA)
    ]]></configfile>

                <option value="paired">paired - in a data set pair</option>
                <option value="separate">paired - in two separate data sets</option>
                <option value="single">single</option>
            </param>
            <when value="paired">
                <param name="reads" argument="fwd/rev" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Paired short read data"/>
            </when>
            <when value="separate">
                <param name="forward" argument="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward read data"/>
                <param name="reverse" argument="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse read data"/>
            </when>
            <when value="single">
                <param name="reads" argument="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
            </when>
        </conditional>
        <expand macro="trimmers"/>
        <expand macro="filters"/>
        <conditional name="seprev_cond">

                <expand macro="trimmers"/>
                <expand macro="filters"/>
            </when>
        </conditional>
        <param argument="rmPhiX" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Discard reads matching the PhiX genome" />
        <param name="orientFwd" argument="orinent.fwd" type="text" value="" optional="true" label="String present at the start of valid reads" help="see below"/>
        <param name="output_statistics" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Output statistics" help="Create extra table with the number of reads pre and post filtering" />
    </inputs>
    <outputs>
        <collection name="paired_output" type="paired">
            <data name="forward" format="fastqsanger.gz" />
            <data name="reverse" format="fastqsanger.gz" />
            <filter>paired_cond['paired_select'] == "paired"</filter>
        </collection>
        <data name="output_single" format="fastqsanger.gz" >
            <filter>paired_cond['paired_select'] == "single"</filter>
        </data>
        <data name="output_fwd" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Forward reads" >
            <filter>paired_cond['paired_select'] == "separate"</filter>
        </data>
		<data name="output_rev" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Reverse reads" >
            <filter>paired_cond['paired_select'] == "separate"</filter>
        </data>
        <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics">
            <filter>output_statistics</filter>
        </data>

        <!-- paired data 
             currently removed `expect_num_outputs="2"` because of https://github.com/galaxyproject/galaxy/pull/7894-->
        <test>
            <conditional name="paired_cond">
                <param name="paired_select" value="paired"/>
                <param name="reads">
                    <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>

        <!-- paired data w separate filters and trimmers for reverse 
             currently removed `expect_num_outputs="1"` because of https://github.com/galaxyproject/galaxy/pull/7894-->
            <test>
            <conditional name="paired_cond">
                <param name="paired_select" value="paired"/>
                <param name="reads">
                    <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>

8:e9d1e654cc9d

fwd <- NULL
rev <- NULL
filt.fwd <- NULL
filt.rev <- NULL
#if $paired_cond.paired_select == "paired"
    fwd <- c(fwd, '$paired_cond.paired_reads.forward')
    rev <- c(rev, '$paired_cond.paired_reads.reverse')
    filt.fwd <- c(filt.fwd, '$paired_output.forward')
    filt.rev <- c(filt.rev, '$paired_output.reverse')
#else if $paired_cond.paired_select == "separate"
    fwd <- c(fwd, '$paired_cond.forward')
    rev <- c(rev, '$paired_cond.reverse')

    truncQ = truncQ, truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight, maxLen = maxLen,
    minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.phix = $rmPhiX, orient.fwd = '$orientFwd')

#if $paired_cond.paired_select == "separate":
    rownames(ftout) <- c( '$paired_cond.forward.element_identifier' )
#else if $paired_cond.paired_select == "paired"
    rownames(ftout) <- c( '$paired_cond.paired_reads.element_identifier' )
#else:
    rownames(ftout) <- c( '$paired_cond.reads.element_identifier' )
#end if
write.table(ftout, "$outtab", quote=F, sep="\t", col.names=NA)
    ]]></configfile>

                <option value="paired">paired - in a data set pair</option>
                <option value="separate">paired - in two separate data sets</option>
                <option value="single">single</option>
            </param>
            <when value="paired">
                <param name="paired_reads" argument="fwd/rev" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired short read data"/>
            </when>
            <when value="separate">
                <param name="forward" argument="fwd" type="data" format="fastq,fastq.gz" label="Forward read data"/>
                <param name="reverse" argument="rev" type="data" format="fastq,fastq.gz" label="Reverse read data"/>
            </when>
            <when value="single">
                <param name="reads" argument="fwd" type="data" format="fastq,fastq.gz" label="Short read data"/>
            </when>
        </conditional>
        <expand macro="trimmers"/>
        <expand macro="filters"/>
        <conditional name="seprev_cond">

                <expand macro="trimmers"/>
                <expand macro="filters"/>
            </when>
        </conditional>
        <param argument="rmPhiX" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Discard reads matching the PhiX genome" />
        <param name="orientFwd" argument="orient.fwd" type="text" value="" optional="true" label="String present at the start of valid reads" help="see below"/>
        <param name="output_statistics" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Output statistics" help="Create extra table with the number of reads pre and post filtering" />
    </inputs>
    <outputs>
        <collection name="paired_output" type="paired" structured_like="paired_reads" inherit_format="true">
            <filter>paired_cond['paired_select'] == "paired"</filter>
        </collection>
        <data name="output_single" format_source="reads" >
            <filter>paired_cond['paired_select'] == "single"</filter>
        </data>
        <data name="output_fwd" format_source="forward" label="${tool.name} on ${on_string}: Forward reads" >
            <filter>paired_cond['paired_select'] == "separate"</filter>
        </data>
        <data name="output_rev" format_source="reverse" label="${tool.name} on ${on_string}: Reverse reads" >
            <filter>paired_cond['paired_select'] == "separate"</filter>
        </data>
        <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics">
            <filter>output_statistics</filter>
        </data>

        <!-- paired data 
             currently removed `expect_num_outputs="2"` because of https://github.com/galaxyproject/galaxy/pull/7894-->
        <test>
            <conditional name="paired_cond">
                <param name="paired_select" value="paired"/>
                <param name="paired_reads">
                    <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>

        <!-- paired data w separate filters and trimmers for reverse 
             currently removed `expect_num_outputs="1"` because of https://github.com/galaxyproject/galaxy/pull/7894-->
            <test>
            <conditional name="paired_cond">
                <param name="paired_select" value="paired"/>
                <param name="paired_reads">
                    <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>