annotate flair_correct.xml @ 0:5d17cf201540 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"

<tool id="flair_correct" name="FLAIR correct" version="@TOOL_VERSION@" profile="20.01">
    <description>corrects misaligned splice sites using genome annotations</description>

    <macros>
        <import>flair_macros.xml</import>
    </macros>

    <expand macro="requirements" />
    <expand macro="version_command" />

    <command detect_errors="exit_code"><![CDATA[

@PREPARE_REF@

flair.py correct

###########
## Input ##
###########

-q '$input_query'
-g reference.fa
-f '$input_gtf'

#if $input_shortread:
    -j '$input_shortread'
#end if

########################
## Additional Options ##
########################

$additional_options.strand
-w $additional_options.window

#########
## END ##
#########

    ]]></command>
    <inputs>
        <param name="input_query" argument="-q" type="data" format="bed12" label="Uncorrected Bed12 file"/>
        <expand macro="reference_interface" />
        <param name="input_gtf" argument="-f" type="data" format="gtf" label="GTF annotation file"/>
        <param name="input_shortread" optional="true" argument="-j" type="data" format="bed" label="Splice junction BED file" />

        <!-- Additional Options -->
        <section name="additional_options" title="Additional Options">
            <param name="strand" argument="-n" type="boolean" checked="false" truevalue="-n" falsevalue="" label="Strand Consistency" help="Keep the strand of a read consistent after correction."/>
            <param name="window" argument="-w" type="integer" min="1" value="10" label="Window Size" help="Window size for correcting splice sites (Default=10)" />
        </section>
    </inputs>


    <outputs>
        <data name="outfile_1" format="bed12" from_work_dir="flair_all_corrected.bed" label="${tool.name} on ${on_string}: Corrected Reads" />
        <data name="outfile_2" format="bed12" from_work_dir="flair_all_inconsistent.bed" label="${tool.name} on ${on_string}: Inconsistent Reads" />
    </outputs>

    <tests>
        <test expect_num_outputs="2">
            <param name="input_query" ftype="bed12" value="chrM.bed12" />
            <param name="ref_selector_genome" value="history" />
            <param name="reffile" ftype="fasta" value="chrM.fa" />
            <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" />
            <output name="outfile_1" ftype="bed12" file="flair_all_corrected.bed" />
            <output name="outfile_2" ftype="bed12" file="flair_all_inconsistent.bed" />
        </test>
        <!-- Test with cached genome -->
        <test expect_num_outputs="2">
            <param name="input_query" ftype="bed12" value="chrM.bed12" />
            <param name="ref_selector_genome" value="cached" />
            <param name="reffile" value="chrM" />
            <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" />
            <output name="outfile_1" ftype="bed12" file="flair_all_corrected.bed" />
            <output name="outfile_2" ftype="bed12" file="flair_all_inconsistent.bed" />
        </test>
    </tests>

    <help><![CDATA[

.. class:: infomark

**What it does**

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

@description@

**flair correct**
Corrects misaligned splice sites using genome annotations and/or short-read splice junctions. Based on common user issues we have encountered, for flair-correct to run properly, please ensure/note that (1) the genome annotation and genome sequences are compatible, (2) gtf is preferred over gff for annotation and annotations that do not split single exons into multiple entries are ideal.

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

**Inputs**

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

(1) Uncorreced bed12 file.
(2) FASTA file of the reference genome.
(3) GTF annotation file.
(4) BED format splice junctions from short-read sequencing or GTF annotation file.

-----------

**Outputs**

-----------

(1) bed12 of corrected reads,
(2) bed12 of reads that weren't able to be corrected,
(3) psl of corrected reads if the -c chromsizes file is provided.

Either (1) or (3) can be supplied to flair-collapse as the query.

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

**More Information**

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

See the excellent `FLAIR documentation`_

.. _`FLAIR documentation`: https://github.com/BrooksLabUCSC/flair


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

**Galaxy Wrapper Development**

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

@citation@

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