Mercurial > repos > nml > gnali
comparison gnali.xml @ 3:02d368ec14cf draft
"planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
| author | nml |
|---|---|
| date | Wed, 13 Jan 2021 18:35:15 +0000 |
| parents | 49012f2b4c19 |
| children | b6e197aac430 |
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| 2:49012f2b4c19 | 3:02d368ec14cf |
|---|---|
| 1 <tool id="gnali" name="gNALI" version="0.1.1" python_template_version="3.6"> | 1 <tool id="gnali" name="gNALI" version="1.0.1" python_template_version="3.7"> |
| 2 <description>Get nonessential, LoF variants</description> | 2 <description>Get nonessential, LoF variants</description> |
| 3 <requirements> | 3 <macros> |
| 4 <requirement type="package" version="0.1.1">gnali</requirement> | 4 <import>macros.xml</import> |
| 5 </requirements> | 5 </macros> |
| 6 <expand macro="requirements" /> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
| 7 gnali -i '$test_genes' -o output | 8 gnali -i '$test_genes' -o output -d '$database_info.database' |
| 9 #if $database_info.predefined_filters != "None": | |
| 10 --predefined_filters '$database_info.predefined_filters' | |
| 11 #end if | |
| 12 #if len($additional_filters) > 0: | |
| 13 --additional_filters | |
| 14 #for $filt in $additional_filters | |
| 15 '$filt.filter' | |
| 16 #end for | |
| 17 #end if | |
| 18 #if $vcf_output: | |
| 19 '$vcf_output' | |
| 20 #end if | |
| 21 #if $pop_freqs: | |
| 22 '$pop_freqs' | |
| 23 #end if | |
| 8 ]]></command> | 24 ]]></command> |
| 9 <inputs> | 25 <inputs> |
| 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" /> | 26 <param type="data" name="test_genes" label="Test genes" format="txt" help="Specify a list of genes as HGNC symbols, separated by newline characters" /> |
| 11 <param type="select" name="database" label="Database" format="txt" help="Database to query" > | 27 <param name="vcf_output" type="boolean" truevalue="--vcf" falsevalue="" optional="false" checked="false" label="VCF output" help="Generate vcf file for filtered variants" /> |
| 12 <option value="gnomad2.1.1" selected="true">gnomAD2.1.1 (GRCh37/hg19)</option> | 28 <param name="pop_freqs" type="boolean" truevalue="--pop_freqs" falsevalue="" optional="false" checked="false" label="Population frequencies" help="Generate population frequency data for variants that passed filtering" /> |
| 13 </param> | 29 <conditional name="database_info"> |
| 30 <param type="select" name="database" label="Database" format="txt" help="Database to query" > | |
| 31 <option value="gnomadv2.1.1" selected="true">gnomADv2.1.1 (GRCh37/hg19)</option> | |
| 32 <option value="gnomadv3">gnomADv3 (GRCh38/hg38)</option> | |
| 33 </param> | |
| 34 <when value="gnomadv2.1.1"> | |
| 35 <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters"> | |
| 36 <option value="homozygous-controls">homozygous controls (controls_nhomalt>0)</option> | |
| 37 <option value="heterozygous-controls">heterozygous controls (controls_nhomalt=0)</option> | |
| 38 <option value="nhomalt>0">homozygous (nhomalt>0)</option> | |
| 39 </param> | |
| 40 </when> | |
| 41 <when value="gnomadv3"> | |
| 42 <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters"> | |
| 43 <option value="homozygous">homozygous (nhomalt>0)</option> | |
| 44 <option value="heterozygous">heterozygous (nhomalt=0)</option> | |
| 45 </param> | |
| 46 </when> | |
| 47 </conditional> | |
| 48 <repeat name="additional_filters" title="Additional filters" min="0" default="0" help="Additional filters (as expressions, ex. AC>10) to apply" > | |
| 49 <param name="filter" type="text" optional="False" label="Filter"> | |
| 50 <sanitizer invalid_char=""> | |
| 51 <valid initial="string.ascii_letters,string.digits"> | |
| 52 <add value=">" /> | |
| 53 <add value="<" /> | |
| 54 <add value="=" /> | |
| 55 </valid> | |
| 56 </sanitizer> | |
| 57 </param> | |
| 58 </repeat> | |
| 14 </inputs> | 59 </inputs> |
| 15 <outputs> | 60 <outputs> |
| 16 <data name="basic_output" label="gNALI basic output" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Basic\).txt" /> | 61 <data name="basic_output" label="gNALI basic output on ${test_genes.element_identifier}" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Basic\).txt" /> |
| 17 <data name="detailed_output" label="gNALI detailed output" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Detailed\).txt" /> | 62 <data name="detailed_output" label="gNALI detailed output on ${test_genes.element_identifier}" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Detailed\).txt" /> |
| 63 <data name="variants_vcf_output" label="gNALI variants vcf on ${test_genes.element_identifier}" format="vcf" from_work_dir="output/Nonessential_Gene_Variants.vcf" > | |
| 64 <filter>vcf_output</filter> | |
| 65 </data> | |
| 18 </outputs> | 66 </outputs> |
| 19 <tests> | 67 <tests> |
| 20 <test> | 68 <test> |
| 21 <param name="test_genes" value="test_genes.txt"/> | 69 <param name="test_genes" value="test_genes.txt"/> |
| 22 <output name="basic_output"> | 70 <param name="predefined_filters" value="homozygous-controls"/> |
| 23 <assert_contents> | 71 <param name="pop_freqs" value="--pop_freqs"/> |
| 24 <has_text text="HGNC_Symbol" /> | 72 <param name="vcf_output" value="--vcf"/> |
| 25 <has_text text="CCR5" /> | 73 <output name="basic_output" |
| 26 </assert_contents> | 74 value="results/Nonessential_Host_Genes_Basic.txt" |
| 75 ftype="txt" | |
| 76 compare="diff"> | |
| 27 </output> | 77 </output> |
| 28 <output name="detailed_output"> | 78 <output name="detailed_output" |
| 29 <assert_contents> | 79 value="results/Nonessential_Host_Genes_Detailed.txt" |
| 30 <has_text_matching expression="Chromosome\tPosition_Start\tRSID\tReference_Allele\tAlternate_Allele\tScore\tQuality\tLoF_Variant\tLoF_Annotation\tHGNC_Symbol\tEnsembl Code" /> | 80 ftype="txt" |
| 31 <has_text_matching expression="3\t46414935\trs938517991\tAT\tA\t9974.16\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" /> | 81 compare="diff"> |
| 32 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t74264261.52\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" /> | |
| 33 <has_text_matching expression="3\t46415066\trs146972949\tC\tT\t120238.89\tPASS\tT\tstop_gained\tCCR5\tENSG00000160791" /> | |
| 34 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t1947603.90\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" /> | |
| 35 </assert_contents> | |
| 36 </output> | 82 </output> |
| 37 </test> | 83 <output name="variants_vcf_output" |
| 38 <test> | 84 value="results/Nonessential_Gene_Variants.vcf" |
| 39 <param name="test_genes" value="patch.txt"/> | 85 ftype="vcf" |
| 40 <output name="basic_output"> | 86 compare="diff"> |
| 41 <assert_contents> | 87 </output> |
| 42 <has_text text="HGNC_Symbol" /> | |
| 43 <has_text text="CCR5" /> | |
| 44 <has_text text="RPEL1" /> | |
| 45 <has_text text="OTOGL" /> | |
| 46 <has_text text="PKD1L2" /> | |
| 47 <has_text text="COL6A5" /> | |
| 48 <has_text text="DCP1A" /> | |
| 49 <has_text text="KRT10" /> | |
| 50 </assert_contents> | |
| 51 </output> | |
| 52 <output name="detailed_output"> | |
| 53 <assert_contents> | |
| 54 <has_text_matching expression="Chromosome\tPosition_Start\tRSID\tReference_Allele\tAlternate_Allele\tScore\tQuality\tLoF_Variant\tLoF_Annotation\tHGNC_Symbol\tEnsembl Code" /> | |
| 55 <has_text_matching expression="10\t105005931\trs61746130\tC\tT\t4480914.72\tPASS\tT\tstop_gained\tRPEL1\tENSG00000235376" /> | |
| 56 <has_text_matching expression="12\t80770908\trs1222716200\tC\tT\t4175.99\tPASS\tT\tstop_gained\tOTOGL\tENSG00000165899" /> | |
| 57 <has_text_matching expression="16\t81242148\trs752607955\tGTT\tG\t218022105.25\tPASS\t-\tframeshift_variant\tPKD1L2\tENSG00000166473" /> | |
| 58 <has_text_matching expression="16\t81242198\trs7499011\tG\tA\t124146106.95\tPASS\tA\tstop_gained\tPKD1L2\tENSG00000166473" /> | |
| 59 <has_text_matching expression="3\t130114290\trs115380050\tC\tT\t105366.23\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" /> | |
| 60 <has_text_matching expression="3\t130139996\trs139339125\tG\tT\t576280.08\tPASS\tT\tsplice_acceptor_variant\tCOL6A5\tENSG00000172752" /> | |
| 61 <has_text_matching expression="3\t130159309\t.\tAAT\tA\t3284.41\tPASS\t-\tframeshift_variant\tCOL6A5\tENSG00000172752" /> | |
| 62 <has_text_matching expression="3\t130159330\trs2201717\tC\tT\t8770317.31\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" /> | |
| 63 <has_text_matching expression="3\t130187662\trs115375867\tG\tT\t1785133.61\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" /> | |
| 64 <has_text_matching expression="3\t130190720\trs11355796\tAT\tA\t157372019.43\tPASS\t-\tframeshift_variant\tCOL6A5\tENSG00000172752" /> | |
| 65 <has_text_matching expression="3\t53324819\trs782498227\tATGGCAC\tA\t304085671.95\tPASS\t-\tsplice_donor_variant&intron_variant\tDCP1A\tENSG00000162290" /> | |
| 66 <has_text_matching expression="3\t46414935\trs938517991\tAT\tA\t9974.16\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" /> | |
| 67 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t74264261.52\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" /> | |
| 68 <has_text_matching expression="3\t46415066\trs146972949\tC\tT\t120238.89\tPASS\tT\tstop_gained\tCCR5\tENSG00000160791" /> | |
| 69 <has_text_matching expression="16\t81242148\trs752607955\tGTT\tG\t12370921.18\tPASS\t-\tframeshift_variant\tPKD1L2\tENSG00000166473" /> | |
| 70 <has_text_matching expression="16\t81242198\trs7499011\tG\tA\t7423817.85\tPASS\tA\tstop_gained\tPKD1L2\tENSG00000166473" /> | |
| 71 <has_text_matching expression="17\t38975327\trs764791942\tT\tTAGCCGCCGCC\t282793.87\tPASS\tAGCCGCCGCC\tframeshift_variant\tKRT10\tENSG00000186395" /> | |
| 72 <has_text_matching expression="17\t38975329\trs762667965\tG\tGAGCTT\t238711.24\tPASS\tAGCTT\tframeshift_variant\tKRT10\tENSG00000186395" /> | |
| 73 <has_text_matching expression="3\t130159330\trs2201717\tC\tT\t165579.83\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" /> | |
| 74 <has_text_matching expression="3\t130190720\trs11355796\tAT\tA\t14066881.99\tPASS\t-\tframeshift_variant\tCOL6A5\tENSG00000172752" /> | |
| 75 <has_text_matching expression="3\t53324819\trs782498227\tATGGCAC\tA\t17202744.04\tPASS\t-\tsplice_donor_variant&intron_variant\tDCP1A\tENSG00000162290" /> | |
| 76 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t1947603.90\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" /> | |
| 77 </assert_contents> | |
| 78 </output> | |
| 79 </test> | 88 </test> |
| 80 </tests> | 89 </tests> |
| 81 <help><![CDATA[ | 90 <help><![CDATA[ |
| 82 | 91 |
| 83 gNALI - Gene Nonessentiality and Loss-of-function Identifier | 92 Introduction |
| 84 ============================================================ | 93 ------------------ |
| 85 | 94 |
| 86 gNALI is a tool to find (high confidence) potential loss-of-function variants of genes. | 95 gNALI (gene nonessentiality and loss-of-function identifier) is a tool to find (high confidence) |
| 96 potential loss of function variants of genes. | |
| 97 | |
| 98 NOTE: loss-of-function is influenced by the genome build. Not all variants available in gnomADv2.1.1 are | |
| 99 available in gnomADv3 and vice versa. | |
| 100 | |
| 101 Usage | |
| 102 ----------- | |
| 103 | |
| 104 Your input file must be of format .csv, .txt, or tsv and should contain a list of genes | |
| 105 (as HGNC symbols) to test, separated by newline characters. | |
| 106 It should not contain any blank lines until the end of the list. | |
| 87 | 107 |
| 88 | 108 |
| 89 Authors | 109 **Population Frequencies** |
| 90 ------- | |
| 91 | 110 |
| 92 gNALI was developed by Xia Liu. | 111 When using the population frequencies feature: |
| 93 | 112 |
| 113 Per population group: | |
| 94 | 114 |
| 95 Usage | 115 * AC denotes allele count |
| 96 ----- | |
| 97 | 116 |
| 98 Accepted input formats: csv, txt, tsv | 117 * AN denotes allele number |
| 99 | 118 |
| 100 Your input file should contain a list of genes (as HGNC symbols) to test, separated by newline characters. | 119 * AF denotes allele frequency |
| 101 It should not contain any blank lines until the end of the list. | |
| 102 | |
| 103 There will be two output files: | |
| 104 | |
| 105 1. A basic output file, containing genes (as HGNC symbols) with nonessential, loss-of-function variants. | |
| 106 2. A detailed output file, with more information on the variants. | |
| 107 | 120 |
| 108 ]]></help> | 121 ]]></help> |
| 109 <citations> | 122 <citations> |
| 110 <citation type="bibtex"> | 123 <citation type="bibtex"> |
| 111 @misc{GitHubgnali, | 124 @misc{GitHubgnali, |