annotate fastq_trim_poly_at.xml @ 0:dcc82e999439 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"

<tool id="fastq_trim_poly_at" name="FASTQ poly-A|T trimmer" profile="18.01" version="0.25.1+galaxy0">
    <description>Trims poly-A stretches at the 3'-end and poly-T at 5'-end of each read, optionally discarding reads with a length below the given threshold.</description>
    <requirements>
        <requirement type="package" version="0.25.1">fastq_utils</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    fastq_trim_poly_at --file '$file' --outfile '$outfile'

    #if '$min_poly_at_len':
        --min_poly_at_len '$min_poly_at_len'
    #end if

    #if '$min_len':
        --min_len '$min_len'
    #end if
    ]]></command>
    <inputs>
        <param name="file" label="Input file"  argument="--file" type="data" format="fastqsanger.gz" optional="false" help="Fastq (optional gzipped) file name"/>
        <param name="min_poly_at_len" label="Minimum Poly-AT Length" argument="--min_poly_at_len" optional="true" type="integer" min="0" help="Minimum length of poly-A|T sequence to remove"/>
        <param name="min_len" label="Minimum Quality" optional="true" value="" argument="--min_qual" type="integer" help="Minimum read length"/>
    </inputs>
    <outputs>
        <data label="${tool.name} on ${on_string}: Output file" name="outfile" format="fastqsanger.gz" />
    </outputs>
    <tests>
        <test>
            <param name="file" value="poly_at.fastq.gz"/>
            <param name="min_poly_at_len" value="3"/>
            <output name="outfile" file="poly_at_len3.fastq.gz" compare="sim_size" delta_frac="0.1"/>
        </test>
    </tests>
    <help><![CDATA[
=======================================================
FASTQ poly-A|T trimmer (fastq_trim_poly_at)
=======================================================

Minimum Poly-AT Length - The terminal poly-A|T sequence
    should be at least this long to be removed

Minimum Length - Reads with post-trimming length less
    than this setting will be removed

     ]]></help>
    <citations>
        <citation type="bibtex"><![CDATA[
            @ARTICLE{Fonseca2017,
            author = {Fonseca, N.},
            title = {fastq_utils},
            year = {2017},
            publisher = {GitHub},
            journal = {GitHub repository},
            howpublished = {\url{https://github.com/nunofonseca/fastq_utils}},
            commit = {c6cf3f954c5286e62fbe36bb9ffecd89d7823b07}
            }]]></citation>
    </citations>
</tool>