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annotate gnali.xml @ 2:49012f2b4c19 draft

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"planemo upload for repository https://github.com/phac-nml/gnali/ commit 5c43f6f0a86589e95959c4d57b60305c8aba548d"
author nml
date Mon, 20 Apr 2020 17:04:56 -0400
parents 3bfa1089a2c4
children 02d368ec14cf
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1 <tool id="gnali" name="gNALI" version="0.1.1" python_template_version="3.6">
0
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2 <description>Get nonessential, LoF variants</description>
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3 <requirements>
2
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4 <requirement type="package" version="0.1.1">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="HGNC_Symbol" />
0
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25 <has_text text="CCR5" />
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26 </assert_contents>
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27 </output>
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28 <output name="detailed_output">
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29 <assert_contents>
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30 <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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31 <has_text_matching expression="3\t46414935\trs938517991\tAT\tA\t9974.16\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
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32 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t74264261.52\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
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33 <has_text_matching expression="3\t46415066\trs146972949\tC\tT\t120238.89\tPASS\tT\tstop_gained\tCCR5\tENSG00000160791" />
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34 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t1947603.90\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
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35 </assert_contents>
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36 </output>
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37 </test>
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38 <test>
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39 <param name="test_genes" value="patch.txt"/>
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40 <output name="basic_output">
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41 <assert_contents>
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42 <has_text text="HGNC_Symbol" />
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43 <has_text text="CCR5" />
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44 <has_text text="RPEL1" />
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45 <has_text text="OTOGL" />
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46 <has_text text="PKD1L2" />
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47 <has_text text="COL6A5" />
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48 <has_text text="DCP1A" />
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49 <has_text text="KRT10" />
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50 </assert_contents>
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51 </output>
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52 <output name="detailed_output">
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53 <assert_contents>
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54 <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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55 <has_text_matching expression="10\t105005931\trs61746130\tC\tT\t4480914.72\tPASS\tT\tstop_gained\tRPEL1\tENSG00000235376" />
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56 <has_text_matching expression="12\t80770908\trs1222716200\tC\tT\t4175.99\tPASS\tT\tstop_gained\tOTOGL\tENSG00000165899" />
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57 <has_text_matching expression="16\t81242148\trs752607955\tGTT\tG\t218022105.25\tPASS\t-\tframeshift_variant\tPKD1L2\tENSG00000166473" />
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58 <has_text_matching expression="16\t81242198\trs7499011\tG\tA\t124146106.95\tPASS\tA\tstop_gained\tPKD1L2\tENSG00000166473" />
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59 <has_text_matching expression="3\t130114290\trs115380050\tC\tT\t105366.23\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" />
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60 <has_text_matching expression="3\t130139996\trs139339125\tG\tT\t576280.08\tPASS\tT\tsplice_acceptor_variant\tCOL6A5\tENSG00000172752" />
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61 <has_text_matching expression="3\t130159309\t.\tAAT\tA\t3284.41\tPASS\t-\tframeshift_variant\tCOL6A5\tENSG00000172752" />
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62 <has_text_matching expression="3\t130159330\trs2201717\tC\tT\t8770317.31\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" />
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63 <has_text_matching expression="3\t130187662\trs115375867\tG\tT\t1785133.61\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" />
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64 <has_text_matching expression="3\t130190720\trs11355796\tAT\tA\t157372019.43\tPASS\t-\tframeshift_variant\tCOL6A5\tENSG00000172752" />
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65 <has_text_matching expression="3\t53324819\trs782498227\tATGGCAC\tA\t304085671.95\tPASS\t-\tsplice_donor_variant&amp;intron_variant\tDCP1A\tENSG00000162290" />
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66 <has_text_matching expression="3\t46414935\trs938517991\tAT\tA\t9974.16\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
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67 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t74264261.52\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
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68 <has_text_matching expression="3\t46415066\trs146972949\tC\tT\t120238.89\tPASS\tT\tstop_gained\tCCR5\tENSG00000160791" />
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69 <has_text_matching expression="16\t81242148\trs752607955\tGTT\tG\t12370921.18\tPASS\t-\tframeshift_variant\tPKD1L2\tENSG00000166473" />
49012f2b4c19 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 5c43f6f0a86589e95959c4d57b60305c8aba548d"
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70 <has_text_matching expression="16\t81242198\trs7499011\tG\tA\t7423817.85\tPASS\tA\tstop_gained\tPKD1L2\tENSG00000166473" />
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71 <has_text_matching expression="17\t38975327\trs764791942\tT\tTAGCCGCCGCC\t282793.87\tPASS\tAGCCGCCGCC\tframeshift_variant\tKRT10\tENSG00000186395" />
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72 <has_text_matching expression="17\t38975329\trs762667965\tG\tGAGCTT\t238711.24\tPASS\tAGCTT\tframeshift_variant\tKRT10\tENSG00000186395" />
49012f2b4c19 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 5c43f6f0a86589e95959c4d57b60305c8aba548d"
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73 <has_text_matching expression="3\t130159330\trs2201717\tC\tT\t165579.83\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" />
49012f2b4c19 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 5c43f6f0a86589e95959c4d57b60305c8aba548d"
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74 <has_text_matching expression="3\t130190720\trs11355796\tAT\tA\t14066881.99\tPASS\t-\tframeshift_variant\tCOL6A5\tENSG00000172752" />
49012f2b4c19 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 5c43f6f0a86589e95959c4d57b60305c8aba548d"
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75 <has_text_matching expression="3\t53324819\trs782498227\tATGGCAC\tA\t17202744.04\tPASS\t-\tsplice_donor_variant&amp;intron_variant\tDCP1A\tENSG00000162290" />
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76 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t1947603.90\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
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77 </assert_contents>
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78 </output>
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79 </test>
0
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80 </tests>
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81 <help><![CDATA[
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82
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83 gNALI - Gene Nonessentiality and Loss-of-function Identifier
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84 ============================================================
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85
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86 gNALI is a tool to find (high confidence) potential loss-of-function variants of genes.
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87
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88
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89 Authors
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90 -------
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91
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92 gNALI was developed by Xia Liu.
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93
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94
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95 Usage
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96 -----
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97
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98 Accepted input formats: csv, txt, tsv
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99
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100 Your input file should contain a list of genes (as HGNC symbols) to test, separated by newline characters.
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101 It should not contain any blank lines until the end of the list.
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102
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103 There will be two output files:
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104
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105 1. A basic output file, containing genes (as HGNC symbols) with nonessential, loss-of-function variants.
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106 2. A detailed output file, with more information on the variants.
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107
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108 ]]></help>
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109 <citations>
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110 <citation type="bibtex">
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111 @misc{GitHubgnali,
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112 author = {Xia, Liu},
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113 year = {2020},
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114 title = {gnali},
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115 publisher = {phac-nml},
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116 journal = {GitHub repository},
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117 url = {https://github.com/phac-nml/gnali/},
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118 }</citation>
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119 </citations>
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120 </tool>
2
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121