comparison tb_profiler_profile.xml @ 2:49b819f88c2b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d

1:5182e1a99313

<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.1.0">
    <description>Infer strain types and drug resistance markers from sequences</description>	
    <requirements>
        <requirement type="package" version="2.1.0">tb-profiler</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
            #if str($fastq_or_bam.input_select.value) == "paired_fastq"
                #set r1_ext = $fastq_or_bam.read1.extension

            && mv results/tbprofiler.results.pdf '${output_pdf}'
        #else if $output_format == "txt"
            && mv results/tbprofiler.results.txt '${output_txt}'
        #end if 

    ]]></command>
    <inputs>
        <param name="platform" type="select" label="Platform">
            <option value="Illumina" selected="true">Illumina</option>
            <option value="minION">MinION</option>
        </param>

            <when value="paired_collection_fastq">
                <param label="Reads (collection)" name="fastq_collection" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
            </when>
            <when value="single_fastq">
                <param label="Reads" name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
            </when>            
            <when value="bam">
                <param name="bam_input" type="data" format="bam" label="Bam" help="Warning!!!: The BAM files must have been created using the ensembl version of the genome."/>
            </when>
        </conditional>
        <param name="output_format" label="Output format" type="select">

                <param label="Quality required for calls to be accepted" type="select" argument="--call_method">
                    <option value="low" selected="true">Low</option>
                    <option value="high">High</option>
                    <option value="optimise">Optimise</option>
                </param>
                <param label="Minimum coverage fraction to infer deletion" type="float"
                        help="Used to infer a deletion if the fraction of a gene covered falls below this value."
                        argument="--min_gene_frac" value="0.9" />

                <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
                <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
                    <option value="bwa" selected="true">bwa</option>
                    <option value="minimap2">minimap2</option>

            <param name="platform" value="Illumina" />
            <param name="options" value="no" />
            <output name="output_txt">
                <assert_contents>
                    <has_line line="Drug-resistance: Drug-resistant" />
		    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
                    <has_line line="rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
                    <has_line line="763031&#009;Rv0667&#009;c.3225T>C&#009;1.000" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_select" value="bam"/>

            <param name="platform" value="Illumina" />
            <param name="options" value="no" />
            <output name="output_txt">
                <assert_contents>
                    <has_line line="Drug-resistance: Drug-resistant" />
		    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
                    <has_line line="rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
                    <has_line line="763031&#009;Rv0667&#009;c.3225T>C&#009;1.000" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[    

The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using SAMtools. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data).

Produces a JSON output file by default.

    ]]></help>
    <citations>
        <citation type="bibtex">
@UNPUBLISHED{Phelan2016,
    author = {Phelan, Jody},
    title = {TBProfiler},

2:49b819f88c2b

<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.4">
    <description>Infer strain types and drug resistance markers from sequences</description>
    <requirements>
        <requirement type="package" version="2.4">tb-profiler</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
            #if str($fastq_or_bam.input_select.value) == "paired_fastq"
                #set r1_ext = $fastq_or_bam.read1.extension

            && mv results/tbprofiler.results.pdf '${output_pdf}'
        #else if $output_format == "txt"
            && mv results/tbprofiler.results.txt '${output_txt}'
        #end if 

    ]]>    </command>
    <inputs>
        <param name="platform" type="select" label="Platform">
            <option value="Illumina" selected="true">Illumina</option>
            <option value="minION">MinION</option>
        </param>

            <when value="paired_collection_fastq">
                <param label="Reads (collection)" name="fastq_collection" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
            </when>
            <when value="single_fastq">
                <param label="Reads" name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
            </when>
            <when value="bam">
                <param name="bam_input" type="data" format="bam" label="Bam" help="Warning!!!: The BAM files must have been created using the ensembl version of the genome."/>
            </when>
        </conditional>
        <param name="output_format" label="Output format" type="select">

                <param label="Quality required for calls to be accepted" type="select" argument="--call_method">
                    <option value="low" selected="true">Low</option>
                    <option value="high">High</option>
                    <option value="optimise">Optimise</option>
                </param>
                <param label="Minimum coverage fraction to infer deletion" type="float" help="Used to infer a deletion if the fraction of a gene covered falls below this value." argument="--min_gene_frac" value="0.9" />

                <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
                <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
                    <option value="bwa" selected="true">bwa</option>
                    <option value="minimap2">minimap2</option>

            <param name="platform" value="Illumina" />
            <param name="options" value="no" />
            <output name="output_txt">
                <assert_contents>
                    <has_line line="Drug-resistance: Drug-resistant" />
                    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
                    <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
                    <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_select" value="bam"/>

            <param name="platform" value="Illumina" />
            <param name="options" value="no" />
            <output name="output_txt">
                <assert_contents>
                    <has_line line="Drug-resistance: Drug-resistant" />
                    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
                    <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
                    <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[    

The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using SAMtools. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data).

Produces a JSON output file by default.

    ]]>    </help>
    <citations>
        <citation type="bibtex">
@UNPUBLISHED{Phelan2016,
    author = {Phelan, Jody},
    title = {TBProfiler},