comparison multiple_join_paired_ends.xml @ 5:e13fb0cbfd8c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380

4:d5db04f46bc2

<tool id="qiime_multiple_join_paired_ends" name="Join paired-end Illumina reads" version="@WRAPPER_VERSION@.0">
    <description>on multiple files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.3.1">fastq-join</requirement>
    </expand>
    <version_command>multiple_join_paired_ends.py -v</version_command>
    <command detect_errors="aggressive"><![CDATA[
        mkdir input
        &&
        #set $match_barcodes = "no"
        #for $i, $s in enumerate( $input_files )
            cp '$s.r1_file' input/forward_${i}.fastq
            &&
            cp '$s.r2_file' input/reverse_${i}.fastq
            &&
            #if str($s.barcode['match_barcodes']) == 'yes'
                #set $match_barcodes = "yes"
                cp '${s.barcode.barcode_seq}' input/barcode_${i}.fastq
                &&
            #end if
        #end for
        multiple_join_paired_ends.py
            --input_dir 'input'
            --output_dir 'output'
            #if $parameter_fp
                --parameter_fp '$parameter_fp'
            #end if
            --read1_indicator 'forward_'
            --read2_indicator 'reverse_'
            #if str($match_barcodes) == 'yes'
                --match_barcodes
                --barcode_indicator 'barcode_'
            #end if
            --leading_text '$leading_text'
            --trailing_text '$trailing_text'
        #for $i, $s in enumerate( $input_files )
            &&
            cp output/forward_${i}/fastqjoin.join.fastq output/${i}_join.fastq
            &&
            cp output/forward_${i}/fastqjoin.un1.fastq output/${i}_un1.fastq
            &&
            cp output/forward_${i}/fastqjoin.un2.fastq output/${i}_un2.fastq
            #if str($s.barcode['match_barcodes']) == 'yes'
                &&
                cp output/forward_${i}/fastqjoin.join_barcodes.fastq output/${i}_barcodes.fastq
            #end if
        #end for
    ]]></command>
    <inputs>
        <repeat name="input_files" title="Input files">
            <param name="r1_file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Forward reads"/>
            <param name="r2_file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Reverse reads"/>

                </when>
                <when value="no"/>
            </conditional>
        </repeat>
        <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior of join_paired_ends.py" optional="true"/>
        <param argument="--leading_text" type="text" value="" label="Leading text to add to each join_paired_ends.py command"/>
        <param argument="--trailing_text" type="text" value="" label="Trailing text to add to each join_paired_ends.py command"/>
    </inputs>
    <outputs>
        <collection name="joined_seq" type="list:list" label="${tool.name} on ${on_string}: Joined sequences">
            <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_(?P&lt;identifier_1&gt;.+).fastq" ext="fastq" directory="output/"/>
        </collection>

5:e13fb0cbfd8c

<tool id="qiime_multiple_join_paired_ends" name="Run join_paired_ends on multiple files" version="@WRAPPER_VERSION@.0">
    <description>(multiple_join_paired_ends)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.3.1">fastq-join</requirement>
    </expand>
    <version_command>multiple_join_paired_ends.py -v</version_command>
    <command detect_errors="aggressive"><![CDATA[
mkdir input
&&
#set $match_barcodes = "no"
#for $i, $s in enumerate( $input_files )
    cp '$s.r1_file' input/forward_${i}.fastq
    &&
    cp '$s.r2_file' input/reverse_${i}.fastq
    &&
    #if str($s.barcode['match_barcodes']) == 'yes'
        #set $match_barcodes = "yes"
        cp '${s.barcode.barcode_seq}' input/barcode_${i}.fastq
        &&
    #end if
#end for
multiple_join_paired_ends.py
    --input_dir 'input'
    --output_dir 'output'
    #if $parameter_fp
        --parameter_fp '$parameter_fp'
    #end if
    --read1_indicator 'forward_'
    --read2_indicator 'reverse_'
    #if str($match_barcodes) == 'yes'
        --match_barcodes
        --barcode_indicator 'barcode_'
    #end if
    --leading_text '$leading_text'
    --trailing_text '$trailing_text'
#for $i, $s in enumerate( $input_files )
    &&
    cp output/forward_${i}/fastqjoin.join.fastq output/${i}_join.fastq
    &&
    cp output/forward_${i}/fastqjoin.un1.fastq output/${i}_un1.fastq
    &&
    cp output/forward_${i}/fastqjoin.un2.fastq output/${i}_un2.fastq
    #if str($s.barcode['match_barcodes']) == 'yes'
        &&
        cp output/forward_${i}/fastqjoin.join_barcodes.fastq output/${i}_barcodes.fastq
    #end if
#end for
    ]]></command>
    <inputs>
        <repeat name="input_files" title="Input files">
            <param name="r1_file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Forward reads"/>
            <param name="r2_file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Reverse reads"/>

                </when>
                <when value="no"/>
            </conditional>
        </repeat>
        <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior of join_paired_ends.py" optional="true"/>
        <param argument="--leading_text" type="text" value="" label="Leading text to add to each join_paired_ends command"/>
        <param argument="--trailing_text" type="text" value="" label="Trailing text to add to each join_paired_ends command"/>
    </inputs>
    <outputs>
        <collection name="joined_seq" type="list:list" label="${tool.name} on ${on_string}: Joined sequences">
            <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_(?P&lt;identifier_1&gt;.+).fastq" ext="fastq" directory="output/"/>
        </collection>