Mercurial > repos > nml > gnali
comparison gnali.xml @ 2:49012f2b4c19 draft
"planemo upload for repository https://github.com/phac-nml/gnali/ commit 5c43f6f0a86589e95959c4d57b60305c8aba548d"
author | nml |
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date | Mon, 20 Apr 2020 17:04:56 -0400 |
parents | 3bfa1089a2c4 |
children | 02d368ec14cf |
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1:3bfa1089a2c4 | 2:49012f2b4c19 |
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1 <tool id="gnali" name="gNALI" version="0.1.0" python_template_version="3.6"> | 1 <tool id="gnali" name="gNALI" version="0.1.1" python_template_version="3.6"> |
2 <description>Get nonessential, LoF variants</description> | 2 <description>Get nonessential, LoF variants</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.1.0">gnali</requirement> | 4 <requirement type="package" version="0.1.1">gnali</requirement> |
5 </requirements> | 5 </requirements> |
6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
7 gnali -i '$test_genes' -o output | 7 gnali -i '$test_genes' -o output |
8 ]]></command> | 8 ]]></command> |
9 <inputs> | 9 <inputs> |
19 <tests> | 19 <tests> |
20 <test> | 20 <test> |
21 <param name="test_genes" value="test_genes.txt"/> | 21 <param name="test_genes" value="test_genes.txt"/> |
22 <output name="basic_output"> | 22 <output name="basic_output"> |
23 <assert_contents> | 23 <assert_contents> |
24 <has_text text="HGNC_Symbol" /> | |
24 <has_text text="CCR5" /> | 25 <has_text text="CCR5" /> |
25 </assert_contents> | 26 </assert_contents> |
26 </output> | 27 </output> |
27 <output name="detailed_output"> | 28 <output name="detailed_output"> |
28 <assert_contents> | 29 <assert_contents> |
31 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t74264261.52\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" /> | 32 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t74264261.52\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" /> |
32 <has_text_matching expression="3\t46415066\trs146972949\tC\tT\t120238.89\tPASS\tT\tstop_gained\tCCR5\tENSG00000160791" /> | 33 <has_text_matching expression="3\t46415066\trs146972949\tC\tT\t120238.89\tPASS\tT\tstop_gained\tCCR5\tENSG00000160791" /> |
33 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t1947603.90\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" /> | 34 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t1947603.90\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" /> |
34 </assert_contents> | 35 </assert_contents> |
35 </output> | 36 </output> |
37 </test> | |
38 <test> | |
39 <param name="test_genes" value="patch.txt"/> | |
40 <output name="basic_output"> | |
41 <assert_contents> | |
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> | |
36 </test> | 79 </test> |
37 </tests> | 80 </tests> |
38 <help><![CDATA[ | 81 <help><![CDATA[ |
39 | 82 |
40 gNALI - Gene Nonessentiality and Loss-of-function Identifier | 83 gNALI - Gene Nonessentiality and Loss-of-function Identifier |
73 journal = {GitHub repository}, | 116 journal = {GitHub repository}, |
74 url = {https://github.com/phac-nml/gnali/}, | 117 url = {https://github.com/phac-nml/gnali/}, |
75 }</citation> | 118 }</citation> |
76 </citations> | 119 </citations> |
77 </tool> | 120 </tool> |
121 |