annotate paired.xml @ 0:40c86e14b674 draft

Uploaded first version of tagdust

<tool id="tagdust_paired_runner_2_31" name="Tagdust paired end runner" version="0.2">
    <description>Runs tagdust in paired end mode</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"></expand>
    <expand macro="stdio"></expand>
    <expand macro="version_command"></expand>
    <command >
        @cat-archiecture@
        cp $read1_file read1.fastq ;
        cp $read2_file read2.fastq ;
        @tagdust-call-minus-files@
            read1.fastq read2.fastq ;
        @ls_and_barcode@
    </command>
    <inputs>
        <param name="read1_file" type="data" format="fastq,fastqsanger" label="Read 1 Fastq file to process" />
        <param name="read2_file" type="data" format="fastq,fastqsanger" label="Read 2 Fastq file to process" />
        <expand macro="reference_source"/>
        <expand macro="architecture"/>
        <expand macro="include_barcode_file"/>
        <expand macro="architecture"></expand>
    </inputs>
    <outputs>
        <data format="txt" name="logfile" label="Tagdust log on ${on_string}." from_work_dir="output/data_logfile.txt"/>
        <data format_source="read1_file" name="extracted1" label="Tagdust extracted Read1 from ${on_string}." from_work_dir="output/data_READ1.fq"/>
        <data format_source="read1_file"  name="unextracted1" label="Tagdust un-extracted Read1 from ${on_string}." from_work_dir="output/data_un_READ1.fq"/>
        <data format_source="read2_file"  name="extracted2" label="Tagdust extracted Read2 from ${on_string}." from_work_dir="output/data_READ2.fq"/>
        <data format_source="read2_file"  name="unextracted2" label="Tagdust un-extracted Read2 from ${on_string}." from_work_dir="output/data_un_READ2.fq"/>
        <expand macro="output_barcode"/>
    </outputs>
    <tests>
        <!-- Large dataset in github but not toolshed -->
        <test>
            <param name="read1_file" value="C75_S29_R1_001_extracted.fastq" ftype="fastq" /> 
            <param name="read2_file" value="C75_S29_R2_001_extracted.fastq" ftype="fastq" /> 
            <param name="architecture" value="R:N" /> 
            <param name="reference_source|reference_source_selector" value="history"/>
            <param name="reference_source|ref_file" value="ercc_and_TPA_mouse_rRNA.fa" ftype="fasta"/>
            <output name="logfile" >
                <assert_contents>
                    <has_text text="Determining threshold for read0." />
                 </assert_contents>
            </output>
            <output name="extracted1" file="C75_S29__READ1.fq" compare="sim_size" delta="10000"/>
            <output name="unextracted1" file="C75_S29__un_READ1.fq"  compare="sim_size" delta="10000"/>
            <output name="extracted2" file="C75_S29__READ2.fq" compare="sim_size" delta="10000"/>
            <output name="unextracted2" file="C75_S29__un_READ2.fq"  compare="sim_size" delta="10000"/>
        </test>
        <test>
            <param name="read1_file" value="read1_extracted.fastq" ftype="fastqsanger" /> 
            <param name="read2_file" value="read2_extracted.fastq" ftype="fastqsanger" /> 
            <param name="architecture" value="test_R:N" /> 
            <param name="reference_source|reference_source_selector" value="history"/>
            <param name="reference_source|ref_file" value="ercc_and_TPA_mouse_rRNA.fa" ftype="fasta"/>
            <output name="logfile" >
                <assert_contents>
                    <has_text text="Determining threshold for read0." />
                 </assert_contents>
            </output>
            <output name="extracted1" file="paired_READ1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/>
            <output name="unextracted1" file="paired_un_READ1.fq"  ftype="fastqsanger" compare="sim_size" delta="1000"/>
            <output name="extracted2" file="paired_READ2.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/>
            <output name="unextracted2" file="paired_un_READ2.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <param name="read1_file" value="read1_extracted.fastq" ftype="fastq" /> 
            <param name="read2_file" value="read2_extracted.fastq" ftype="fastq" /> 
            <param name="architecture" value="test_R:N" /> 
            <param name="reference_source|reference_source_selector" value="cached"/>
            <param name="ref_path" value="test_ercc_and_TPA_mouse_RNA"/>
            <output name="logfile" >
                <assert_contents>
                    <has_text text="Determining threshold for read0." />
                 </assert_contents>
            </output>
            <output name="extracted1" file="paired_READ1.fq" compare="sim_size" delta="1000"/>
            <output name="unextracted1" file="paired_un_READ1.fq"  compare="sim_size" delta="1000"/>
            <output name="extracted2" file="paired_READ2.fq" compare="sim_size" delta="1000"/>
            <output name="unextracted2" file="paired_un_READ2.fq"  compare="sim_size" delta="1000"/>
        </test>
    </tests>
    <help>
<![CDATA[
This tool runs Tagdust2 in paired end mode.

]]>
@tool-documentation@

@tagdust-documentation@

    </help> 
    <expand macro="citations"></expand>
</tool>