comparison macros_process.xml @ 2:d033e1ccb386 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"

1:21d2aa544835

        </param>
    </xml>

    <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>

    <xml name="process_outputs">
        <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads">
            <filter>input_type['input_type_select'] == "single"</filter>

            <param name="filter_select" type="select" label="Do quality filtering">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
                <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1" />
                <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded" />
                <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" />
                <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
                <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing" />
            </when>
            <when value="no">
                <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="useful if your data has already been trimmed"/>
            </when>
        </conditional>
        <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
    </xml>
    <token name="@PROCESS_FILTER@"><![CDATA[
    #if $filter_cond.filter_select == 'yes':
        -w $filter_cond.sliding
        -s $filter_cond.score

        && mkdir stacks_outputs/discarded/
        && mv stacks_outputs/*discards stacks_outputs/discarded/

        ## fix the _R[12]_0 that was added for preparing the input
        #if $input_type.input_type_select == 'paired':
            && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done
        #end if
        ## also remove the gz which is added by procrad (but its uncompressed)
        && find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done

        ## the discard files are named fastq even if the output is fasta
        #if str($outype).endswith("fasta"):
            && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done
        #else
            && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done
        #end if
    #end if
    ## prepare paired read output for processing in galaxy
    #if $input_type.input_type_select == 'paired':
        && mkdir stacks_outputs/remaining
        && find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done
        && find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done
    #end if
    ]]></token>

    <!-- adapter trimming options -->
    <xml name="process_adapter">
            <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read" />
            <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read" />
            <param argument="--adapter_mm" type="integer" value="" optional="true" label="Number of mismatches allowed in the adapter sequence"/>
    </xml>
    <token name="@PROCESS_ADAPTER@"><![CDATA[
    ## Adapter options
    #if str($options_advanced.adapter_1) != "":

    #end if
    ]]></token>

    <!-- advanced options that are shared -->
    <xml name="common_advanced">
        <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
        <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output" />
    </xml>
    <token name="@COMMON_ADVANCED@"><![CDATA[
    #if str($options_advanced.truncate)
        -t $options_advanced.truncate
    #end if
    $options_advanced.retain_header
    ]]></token>
</macros>

2:d033e1ccb386

        </param>
    </xml>

    <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>

    <xml name="process_outputs">
        <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads">
            <filter>input_type['input_type_select'] == "single"</filter>

            <param name="filter_select" type="select" label="Do quality filtering">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
                <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1"/>
                <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded"/>
                <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base"/>
                <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
                <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing"/>
            </when>
            <when value="no">
                <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="useful if your data has already been trimmed"/>
            </when>
        </conditional>
        <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/>
    </xml>
    <token name="@PROCESS_FILTER@"><![CDATA[
    #if $filter_cond.filter_select == 'yes':
        -w $filter_cond.sliding
        -s $filter_cond.score

        && mkdir stacks_outputs/discarded/
        && mv stacks_outputs/*discards stacks_outputs/discarded/

        ## fix the _R[12]_0 that was added for preparing the input
        #if $input_type.input_type_select == 'paired':
            && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done)
        #end if
        ## also remove the gz which is added by procrad (but its uncompressed)
        && (find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done)

        ## the discard files are named fastq even if the output is fasta
        #if str($outype).endswith("fasta"):
            && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done)
        #else
            && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done)
        #end if
    #end if
    ## prepare paired read output for processing in galaxy
    #if $input_type.input_type_select == 'paired':
        && mkdir stacks_outputs/remaining
        && (find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done)
        && (find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done)
    #end if
    ]]></token>

    <!-- adapter trimming options -->
    <xml name="process_adapter">
            <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read"/>
            <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read"/>
            <param argument="--adapter_mm" type="integer" value="" optional="true" label="Number of mismatches allowed in the adapter sequence"/>
    </xml>
    <token name="@PROCESS_ADAPTER@"><![CDATA[
    ## Adapter options
    #if str($options_advanced.adapter_1) != "":

    #end if
    ]]></token>

    <!-- advanced options that are shared -->
    <xml name="common_advanced">
        <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value"/>
        <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output"/>
    </xml>
    <token name="@COMMON_ADVANCED@"><![CDATA[
    #if str($options_advanced.truncate)
        -t $options_advanced.truncate
    #end if
    $options_advanced.retain_header
    ]]></token>
</macros>