annotate gnali.xml @ 2:49012f2b4c19 draft

"planemo upload for repository https://github.com/phac-nml/gnali/ commit 5c43f6f0a86589e95959c4d57b60305c8aba548d"

<tool id="gnali" name="gNALI" version="0.1.1" python_template_version="3.6">
    <description>Get nonessential, LoF variants</description>
    <requirements>
        <requirement type="package" version="0.1.1">gnali</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        gnali -i '$test_genes' -o output
    ]]></command>
    <inputs>
        <param type="data" name="test_genes" label="Test genes" format="txt" help="Specify a list of genes as HGNC symbols, separated by newline characters" />
        <param type="select" name="database" label="Database" format="txt" help="Database to query" >
            <option value="gnomad2.1.1" selected="true">gnomAD2.1.1 (GRCh37/hg19)</option>
        </param>
    </inputs>
    <outputs>
        <data name="basic_output" label="gNALI basic output" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Basic\).txt" />
        <data name="detailed_output" label="gNALI detailed output" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Detailed\).txt" />
    </outputs>
    <tests>
        <test>
            <param name="test_genes" value="test_genes.txt"/>
            <output name="basic_output">
                <assert_contents>
                    <has_text text="HGNC_Symbol" />
                    <has_text text="CCR5" />
                </assert_contents>
            </output>
            <output name="detailed_output">
                <assert_contents>
                    <has_text_matching expression="Chromosome\tPosition_Start\tRSID\tReference_Allele\tAlternate_Allele\tScore\tQuality\tLoF_Variant\tLoF_Annotation\tHGNC_Symbol\tEnsembl Code" />
                    <has_text_matching expression="3\t46414935\trs938517991\tAT\tA\t9974.16\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
                    <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t74264261.52\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
                    <has_text_matching expression="3\t46415066\trs146972949\tC\tT\t120238.89\tPASS\tT\tstop_gained\tCCR5\tENSG00000160791" />
                    <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t1947603.90\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="test_genes" value="patch.txt"/>
                <output name="basic_output">
                    <assert_contents>
                        <has_text text="HGNC_Symbol" />
                        <has_text text="CCR5" />
                        <has_text text="RPEL1" />
                        <has_text text="OTOGL" />
                        <has_text text="PKD1L2" />
                        <has_text text="COL6A5" />
                        <has_text text="DCP1A" />
                        <has_text text="KRT10" />
                    </assert_contents>
                </output>
                <output name="detailed_output">
                    <assert_contents>
                        <has_text_matching expression="Chromosome\tPosition_Start\tRSID\tReference_Allele\tAlternate_Allele\tScore\tQuality\tLoF_Variant\tLoF_Annotation\tHGNC_Symbol\tEnsembl Code" />
                        <has_text_matching expression="10\t105005931\trs61746130\tC\tT\t4480914.72\tPASS\tT\tstop_gained\tRPEL1\tENSG00000235376" />
                        <has_text_matching expression="12\t80770908\trs1222716200\tC\tT\t4175.99\tPASS\tT\tstop_gained\tOTOGL\tENSG00000165899" />
                        <has_text_matching expression="16\t81242148\trs752607955\tGTT\tG\t218022105.25\tPASS\t-\tframeshift_variant\tPKD1L2\tENSG00000166473" />
                        <has_text_matching expression="16\t81242198\trs7499011\tG\tA\t124146106.95\tPASS\tA\tstop_gained\tPKD1L2\tENSG00000166473" />
                        <has_text_matching expression="3\t130114290\trs115380050\tC\tT\t105366.23\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" />
                        <has_text_matching expression="3\t130139996\trs139339125\tG\tT\t576280.08\tPASS\tT\tsplice_acceptor_variant\tCOL6A5\tENSG00000172752" />
                        <has_text_matching expression="3\t130159309\t.\tAAT\tA\t3284.41\tPASS\t-\tframeshift_variant\tCOL6A5\tENSG00000172752" />
                        <has_text_matching expression="3\t130159330\trs2201717\tC\tT\t8770317.31\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" />
                        <has_text_matching expression="3\t130187662\trs115375867\tG\tT\t1785133.61\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" />
                        <has_text_matching expression="3\t130190720\trs11355796\tAT\tA\t157372019.43\tPASS\t-\tframeshift_variant\tCOL6A5\tENSG00000172752" />
                        <has_text_matching expression="3\t53324819\trs782498227\tATGGCAC\tA\t304085671.95\tPASS\t-\tsplice_donor_variant&amp;intron_variant\tDCP1A\tENSG00000162290" />
                        <has_text_matching expression="3\t46414935\trs938517991\tAT\tA\t9974.16\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
                        <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t74264261.52\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
                        <has_text_matching expression="3\t46415066\trs146972949\tC\tT\t120238.89\tPASS\tT\tstop_gained\tCCR5\tENSG00000160791" />
                        <has_text_matching expression="16\t81242148\trs752607955\tGTT\tG\t12370921.18\tPASS\t-\tframeshift_variant\tPKD1L2\tENSG00000166473" />
                        <has_text_matching expression="16\t81242198\trs7499011\tG\tA\t7423817.85\tPASS\tA\tstop_gained\tPKD1L2\tENSG00000166473" />
                        <has_text_matching expression="17\t38975327\trs764791942\tT\tTAGCCGCCGCC\t282793.87\tPASS\tAGCCGCCGCC\tframeshift_variant\tKRT10\tENSG00000186395" />
                        <has_text_matching expression="17\t38975329\trs762667965\tG\tGAGCTT\t238711.24\tPASS\tAGCTT\tframeshift_variant\tKRT10\tENSG00000186395" />
                        <has_text_matching expression="3\t130159330\trs2201717\tC\tT\t165579.83\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" />
                        <has_text_matching expression="3\t130190720\trs11355796\tAT\tA\t14066881.99\tPASS\t-\tframeshift_variant\tCOL6A5\tENSG00000172752" />
                        <has_text_matching expression="3\t53324819\trs782498227\tATGGCAC\tA\t17202744.04\tPASS\t-\tsplice_donor_variant&amp;intron_variant\tDCP1A\tENSG00000162290" />
                        <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t1947603.90\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
                    </assert_contents>
                </output>
        </test>
    </tests>
    <help><![CDATA[

gNALI - Gene Nonessentiality and Loss-of-function Identifier
============================================================

gNALI is a tool to find (high confidence) potential loss-of-function variants of genes.


Authors
-------

gNALI was developed by Xia Liu.


Usage
-----

Accepted input formats: csv, txt, tsv

Your input file should contain a list of genes (as HGNC symbols) to test, separated by newline characters.
It should not contain any blank lines until the end of the list.

There will be two output files:

    1. A basic output file, containing genes (as HGNC symbols) with nonessential, loss-of-function variants.
    2. A detailed output file, with more information on the variants.

    ]]></help>
    <citations>
        <citation type="bibtex">
    @misc{GitHubgnali,
    author = {Xia, Liu},
    year = {2020},
    title = {gnali},
    publisher = {phac-nml},
    journal = {GitHub repository},
    url = {https://github.com/phac-nml/gnali/},
    }</citation>
    </citations>
</tool>