comparison slamdunk.xml @ 1:57bf9a0d49a5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93

0:3fd7458bc861

<tool id="slamdunk" name="Slamdunk" version="0.3.3">
    <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description>
    <requirements>
        <requirement type="package" version="0.3.3">slamdunk</requirement>
    </requirements>
    <version_command>slamdunk --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
    #if $reference_source.reference_source_selector == 'history':
        ln -f -s '$reference_source.ref_file' reference.fa &&
    #else:

        -rl $readLength
        -c $covThresh
        '$Reads'
    ]]></command>
    <inputs>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Genome" help="Select a built-in FASTA file (if available) or one from the history">
                <option value="cached">Use a built-in FASTA</option>
                <option value="history">Use a FASTA from history</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Use built-in FASTA" help="Select genome from the list">
                    <options from_data_table="all_fasta">
                        <filter type="sort_by" column="2" />
                        <validator type="no_options" message="No reference genomes are available" />
                    </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the FASTA" help="You can upload a FASTA sequence to the history and use it as reference" />
            </when>
        </conditional>
        <param name="Reference" type="data" format="bed" />
        <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" />
        <section name="multimapper" title="Multimapper recovery"
            expanded="false">
            <section name="filterbed"
                title="Use separate 3' UTR bed to filter multimappers." expanded="false">
                <param name="bedtofilter" type="data" format="bed" optional="true"

                label="Enable end-to-end alignments for mapping."
                help="Enable end-to-end alignments for mapping in slamdunk with --endtoend" />
            <param name="minMQ" type="integer" min="0" value="2"
                label="Minimum mapping quality"
                help="Minimum mapping quality to consider alignments (default: 2)." />
            <param name="minMQ" type="integer" label="Minimum mapping quality" min="0" value="2"
                help="Minimum mapping quality to consider alignments (default: 2)." />
            <param name="minID" type="float" min="0" value="0.95"
                label="Minimum alignment identity"
                help="Minimum alignment-identity to consider alignments (default: 0.95)." />
            <param name="maxNM" type="integer" value="-1"
                label="Maximum number of mismatches"

        <param name="readLength" type="integer" min="50" value="50"
            label="Read length"
            help="Maximum read length (before trimming)." />
    </inputs>
    <outputs>
        <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" />
        <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" />
    </outputs>
    <tests>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" value="ref.fa" />
            <param name="Reference" value="actb.bed" />
            <param name="Reads" value="reads.fq" />
            <param name="readLength" value="100" />

                <param name="trim5" value="0" />
            </section>
            <section name="advanced">
                <param name="minBaseQual" value="27" />
            </section>
            <output name="outputTsv" file="reads_slamdunk_mapped_filtered_tcount.tsv"
                lines_diff="2" />
        </test>
        <test>
            <!-- test built-in fasta -->
            <param name="reference_source_selector" value="cached" />
            <param name="Reference" value="actb.bed" />
            <param name="Reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
            <param name="readLength" value="100" />
            <section name="quantseq">
                <param name="trim5" value="0" />
            </section>
            <section name="advanced">
                <param name="minBaseQual" value="27" />
            </section>
            <output name="outputTsv" file="reads_slamdunk_mapped_filtered_tcount.tsv"
                lines_diff="2" />
        </test>
    </tests>
    <help><![CDATA[
SLAM-seq
========

**Reference**    BED-file containing coordinates for 3' UTRs.
**Reads**        Sample FASTQ(gz) files.
**Read length**  Maximum length of reads (usually 50, 100, 150).
===============  ==========================================================================================================================================================

This will run the entire *slamdunk* analysis with the most relevant output files being:

* Tab-separated *tcount* file containing the SLAM-seq statistics per UTR
* BAM-file with the final mapped reads for visualization and further processing

------------------------------------------------------

Multimapper recovery
--------------------

Parameter  Description
============================  ================================================================================
**T>C conversion threshold**  Minimum number of T>C conversions to consider a read as T>C read.
============================  ================================================================================


    ]]></help>
    <citations>
        <citation type="bibtex">
 @misc{Neumann2018,
  author = {Neumann, Tobias},
  year = {2018},
  title = Slamdunk},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/t-neumann/slamdunk},
}
        </citation>
    </citations>
</tool>

1:57bf9a0d49a5

<tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy1">
    <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>slamdunk --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
    #if $reference_source.reference_source_selector == 'history':
        ln -f -s '$reference_source.ref_file' reference.fa &&
    #else:

        -rl $readLength
        -c $covThresh
        '$Reads'
    ]]></command>
    <inputs>
        <expand macro="reference_files" />
        <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ files"/>
        <section name="multimapper" title="Multimapper recovery"
            expanded="false">
            <section name="filterbed"
                title="Use separate 3' UTR bed to filter multimappers." expanded="false">
                <param name="bedtofilter" type="data" format="bed" optional="true"

                label="Enable end-to-end alignments for mapping."
                help="Enable end-to-end alignments for mapping in slamdunk with --endtoend" />
            <param name="minMQ" type="integer" min="0" value="2"
                label="Minimum mapping quality"
                help="Minimum mapping quality to consider alignments (default: 2)." />
            <param name="minID" type="float" min="0" value="0.95"
                label="Minimum alignment identity"
                help="Minimum alignment-identity to consider alignments (default: 0.95)." />
            <param name="maxNM" type="integer" value="-1"
                label="Maximum number of mismatches"

        <param name="readLength" type="integer" min="50" value="50"
            label="Read length"
            help="Maximum read length (before trimming)." />
    </inputs>
    <outputs>
        <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" label="${tool.name} on ${on_string}: BAM"/>
        <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" label="${tool.name} on ${on_string}: Count TSV"/>
        <data name="outputVcf" format="vcf" from_work_dir="./out/snp/*vcf" label="${tool.name} on ${on_string}: VCF"/>
    </outputs>
    <tests>
        <test>
            <!--Ensure default outputs work -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" value="ref.fa" />
            <param name="Reference" value="actb.bed" />
            <param name="Reads" value="reads.fq" />
            <param name="readLength" value="100" />

                <param name="trim5" value="0" />
            </section>
            <section name="advanced">
                <param name="minBaseQual" value="27" />
            </section>
            <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/>
            <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
                lines_diff="2" />
            <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/>
        </test>
        <test>
            <!--Ensure built-in fasta works -->
            <param name="reference_source_selector" value="cached" />
            <param name="Reference" value="actb.bed" />
            <param name="Reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
            <param name="readLength" value="100" />
            <section name="quantseq">
                <param name="trim5" value="0" />
            </section>
            <section name="advanced">
                <param name="minBaseQual" value="27" />
            </section>
            <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/>
            <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
                lines_diff="2" />
            <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
SLAM-seq
========

**Reference**    BED-file containing coordinates for 3' UTRs.
**Reads**        Sample FASTQ(gz) files.
**Read length**  Maximum length of reads (usually 50, 100, 150).
===============  ==========================================================================================================================================================

This will run the entire *slamdunk* analysis (`slamdunk all`) with the most relevant output files being:

* Tab-separated *tcount* file (Count TSV) containing the SLAM-seq statistics per UTR
* BAM-file with the final filtered mapped reads
* VCF file of variants called on the final filtered alignments

These files can be input to the **Alleyoop** tool for visualization and further processing. See the `Slamdunk documentation`_ for more information.

------------------------------------------------------

Multimapper recovery
--------------------

Parameter  Description
============================  ================================================================================
**T>C conversion threshold**  Minimum number of T>C conversions to consider a read as T>C read.
============================  ================================================================================

.. _`Slamdunk documentation`: http://t-neumann.github.io/slamdunk/docs.html

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