comparison macros_process.xml @ 5:09b8edb56d80 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"

4:d9bf483266a1

<!-- macros and tokens for process_radtags and process_short_reads -->

<macros>

    <token name="@PROCESS_IOOPTIONS@"><![CDATA[
    -p stacks_inputs/
    #if $input_type.input_type_select == "paired"
        --paired
    #end if
    -i $inputype
    -b '$barcode'
    $input_type.barcode_encoding
    #if str( $outype ) != "auto"
        -y $outype
    #end if
    -o stacks_outputs
    ]]></token>

        <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 ${on_string} Demultiplexed reads">
            <filter>input_type['input_type_select'] == "single"</filter>
            <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;name&gt;.+)" dir="stacks_outputs"/>
        </collection>
        <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads">
            <filter>input_type['input_type_select'] == "paired"</filter>
            <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs"/>
        </collection>

        <collection name="remaining" type="list:paired" label="${tool.name} on ${on_string} Remaining orphan reads">
            <filter>input_type['input_type_select'] == "paired"</filter>
            <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.rem\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs/remaining"/>
        </collection>

        <!-- note irrespective of -y output is always named fastq and are never zipped -->
        <collection name="discarded" type="list" label="${tool.name} on ${on_string} Discarded reads">
            <filter>capture is True and input_type['input_type_select'] == "single"</filter>
            <expand macro="discover_faq_output_macro" pattern="(?P&lt;name&gt;.*)" dir="stacks_outputs/discarded"/>
        </collection>

                <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[

5:09b8edb56d80

<!-- macros and tokens for process_radtags and process_short_reads -->

<macros>

  
    <token name="@PROCESS_IOOPTIONS@"><![CDATA[
    -p stacks_inputs/
    #if $input_type.input_type_select == "paired"
        --paired
    #end if
    -i $inputype
    $input_type.barcode_encoding
    #if $input_type.barcode_encoding != ''
        -b '$input_type.barcode'
    #end if
    #if str( $outype ) != "auto"
        -y $outype
    #end if
    -o stacks_outputs
    ]]></token>

        <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/"/>
        <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/"/>
    </xml>

    <xml name="process_outputs">
        <yield/>
        <collection name="remaining" type="list:paired" label="${tool.name} on ${on_string} Remaining orphan reads">
            <filter>input_type['input_type_select'] == "paired"</filter>
            <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.rem\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs/remaining"/>
        </collection>
        <!-- note irrespective of -y output is always named fastq and are never zipped -->
        <collection name="discarded" type="list" label="${tool.name} on ${on_string} Discarded reads">
            <filter>capture is True and input_type['input_type_select'] == "single"</filter>
            <expand macro="discover_faq_output_macro" pattern="(?P&lt;name&gt;.*)" dir="stacks_outputs/discarded"/>
        </collection>

                <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[