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annotate gnali.xml @ 0:9ca12bc2be43 draft

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"planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
author nml
date Mon, 30 Mar 2020 11:48:21 -0400
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children 3bfa1089a2c4
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9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
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1 <tool id="gnali" name="gNALI" version="0.1.0" python_template_version="3.6">
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2 <description>Get nonessential, LoF variants</description>
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3 <requirements>
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4 <requirement type="package" version="0.1">gnali</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 gnali -i '$test_genes' -o output
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8 ]]></command>
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9 <inputs>
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10 <param type="data" name="test_genes" label="Test genes" format="txt" help="Specify a list of genes as HGNC symbols, separated by newline characters" />
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11 <param type="select" name="database" label="Database" format="txt" help="Database to query" >
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12 <option value="gnomad2.1.1" selected="true">gnomAD2.1.1 (GRCh37/hg19)</option>
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13 </param>
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14 </inputs>
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15 <outputs>
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16 <data name="basic_output" label="gNALI basic output" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Basic\).txt" />
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17 <data name="detailed_output" label="gNALI detailed output" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Detailed\).txt" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="test_genes" value="test_genes.txt"/>
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22 <output name="basic_output">
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23 <assert_contents>
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24 <has_text text="CCR5" />
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25 </assert_contents>
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26 </output>
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27 <output name="detailed_output">
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28 <assert_contents>
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29 <has_text_matching expression="Chromosome\tPosition_Start\tRSID\tReference_Allele\tAlternate_Allele\tScore\tQuality\tLoF_Variant\tLoF_Annotation\tHGNC_Symbol\tEnsembl Code" />
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30 <has_text_matching expression="3\t46414935\trs938517991\tAT\tA\t9974.16\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
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31 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t74264261.52\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
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32 <has_text_matching expression="3\t46415066\trs146972949\tC\tT\t120238.89\tPASS\tT\tstop_gained\tCCR5\tENSG00000160791" />
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33 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t1947603.90\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
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34 </assert_contents>
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35 </output>
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39
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40 gNALI - Gene Nonessentiality and Loss-of-function Identifier
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41 ============================================================
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42
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43 gNALI is a tool to find (high confidence) potential loss-of-function variants of genes.
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44
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45
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46 Authors
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47 -------
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48
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49 gNALI was developed by Xia Liu.
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50
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51
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52 Usage
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53 -----
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54
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55 Accepted input formats: csv, txt, tsv
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56
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57 Your input file should contain a list of genes (as HGNC symbols) to test, separated by newline characters.
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58 It should not contain any blank lines until the end of the list.
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59
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60 There will be two output files:
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61
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62 1. A basic output file, containing genes (as HGNC symbols) with nonessential, loss-of-function variants.
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63 2. A detailed output file, with more information on the variants.
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64
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65 ]]></help>
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66 <citations>
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67 <citation type="bibtex">
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68 @misc{GitHubgnali,
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69 author = {Xia, Liu},
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70 year = {2020},
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71 title = {gnali},
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72 publisher = {phac-nml},
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73 journal = {GitHub repository},
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74 url = {https://github.com/phac-nml/gnali/},
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75 }</citation>
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76 </citations>
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77 </tool>