annotate single.xml @ 0:40c86e14b674 draft

Uploaded first version of tagdust

<tool id="tagdust_single_runner_2_31" name="Tagdust single end runner" version="0.2">
    <description>Runs tagdust in single end mode</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command >
        @cat-archiecture@
        cp $fastq_file input.fastq ;
        @tagdust-call-minus-files@
            input.fastq ;
        @ls_and_barcode@
    </command>
    <inputs>
        <param name="fastq_file" type="data" format="fastq,fastqsanger" label="Fastq file to process" />
        <expand macro="reference_source"/>
        <expand macro="architecture"/>
        <expand macro="include_barcode_file"/>
    </inputs>
    <outputs>
        <data format="txt" name="logfile" label="Tagdust log on ${on_string} ." from_work_dir="output/data_logfile.txt"/>
        <data format_source="fastq_file" name="extracted" label="Tagdust extracted reads from ${on_string}." from_work_dir="output/data.fq"/>
        <data format_source="fastq_file" name="unextracted" label="Tagdust un-extracted reads from ${on_string}." from_work_dir="output/data_un.fq"/>
        <expand macro="output_barcode"/>
    </outputs>
    <tests>
        <!-- Large dataset in github but not toolshed -->
        <!--test>
            <param name="fastq_file" value="C75_S29_R1_001.fastq" ftype="fastq" /> 
            <param name="architecture" value="F:NNNNNNNN_S:TATAGGG_R:N" /> 
            <param name="include|barcode_files" value="no" /> 
            <output name="logfile" >
                <assert_contents>
                    <has_text text="Determining threshold for read0." />
                 </assert_contents>
            </output>
            <output name="extracted" file="C75_S29_R1_001.fq" compare="sim_size" delta="10000"/>
            <output name="unextracted" file="C75_S29_R1_001_un.fq"  compare="sim_size" delta="10000"/>
        </test-->
        <test>
            <param name="fastq_file" value="read1.fastq" ftype="fastqsanger" /> 
            <param name="architecture" value="test_F:NNNNNNNN_S:TATAGGG_R:N" /> 
            <param name="barcode_files" value="no" /> 
            <output name="logfile" >
                <assert_contents>
                    <has_text text="Determining threshold for read0." />
                 </assert_contents>
            </output>
            <output name="extracted" file="read1.fq"  ftype="fastqsanger" compare="sim_size" delta="1000"/>
            <output name="unextracted" file="read1_un.fq"  ftype="fastqsanger" compare="sim_size" delta="1000"/>
        </test>
        <test>
            <param name="run_type_selector" value="single"/> 
            <param name="fastq_file" value="read1.fastq" ftype="fastq" /> 
            <param name="architecture" value="test_B:GTA_AAC_R:N" /> 
            <param name="include|barcode_files" value="yes" /> 
            <output name="logfile" >
                <assert_contents>
                    <has_text text="Determining threshold for read0." />
                 </assert_contents>
            </output>
            <output name="extracted" file="with_b_.fq"/>
            <output name="unextracted" file="with_b_un.fq"/>
            <output name="barcode_files">
                <assert_contents>
                    <has_line line="data_BC_AAC.fq" />
                    <has_line line="data_BC_GTA.fq" />
                </assert_contents>
                <discovered_dataset designation="AAC" ftype="fastq" file="with_b_BC_AAC.fq"/>
                <discovered_dataset designation="GTA" ftype="fastq" file="with_b_BC_GTA.fq"/>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
This tool runs Tagdust2 in single mode.

]]>
@tool-documentation@

@tagdust-documentation@

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