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comparison 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
comparison
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1:3bfa1089a2c4 2:49012f2b4c19
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&amp;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&amp;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