# HG changeset patch
# User nml
# Date 1587416696 14400
# Node ID 49012f2b4c192c03eec04c7f355d73e5094eae7c
# Parent  3bfa1089a2c4291532307326d929856d187a7433
"planemo upload for repository https://github.com/phac-nml/gnali/ commit 5c43f6f0a86589e95959c4d57b60305c8aba548d"

diff -r 3bfa1089a2c4 -r 49012f2b4c19 gnali.xml
--- a/gnali.xml	Tue Mar 31 14:22:49 2020 -0400
+++ b/gnali.xml	Mon Apr 20 17:04:56 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="gnali" name="gNALI" version="0.1.0" python_template_version="3.6">
+<tool id="gnali" name="gNALI" version="0.1.1" python_template_version="3.6">
     <description>Get nonessential, LoF variants</description>
     <requirements>
-        <requirement type="package" version="0.1.0">gnali</requirement>
+        <requirement type="package" version="0.1.1">gnali</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         gnali -i '$test_genes' -o output
@@ -21,6 +21,7 @@
             <param name="test_genes" value="test_genes.txt"/>
             <output name="basic_output">
                 <assert_contents>
+                    <has_text text="HGNC_Symbol" />
                     <has_text text="CCR5" />
                 </assert_contents>
             </output>
@@ -34,6 +35,48 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="test_genes" value="patch.txt"/>
+                <output name="basic_output">
+                    <assert_contents>
+                        <has_text text="HGNC_Symbol" />
+                        <has_text text="CCR5" />
+                        <has_text text="RPEL1" />
+                        <has_text text="OTOGL" />
+                        <has_text text="PKD1L2" />
+                        <has_text text="COL6A5" />
+                        <has_text text="DCP1A" />
+                        <has_text text="KRT10" />
+                    </assert_contents>
+                </output>
+                <output name="detailed_output">
+                    <assert_contents>
+                        <has_text_matching expression="Chromosome\tPosition_Start\tRSID\tReference_Allele\tAlternate_Allele\tScore\tQuality\tLoF_Variant\tLoF_Annotation\tHGNC_Symbol\tEnsembl Code" />
+                        <has_text_matching expression="10\t105005931\trs61746130\tC\tT\t4480914.72\tPASS\tT\tstop_gained\tRPEL1\tENSG00000235376" />
+                        <has_text_matching expression="12\t80770908\trs1222716200\tC\tT\t4175.99\tPASS\tT\tstop_gained\tOTOGL\tENSG00000165899" />
+                        <has_text_matching expression="16\t81242148\trs752607955\tGTT\tG\t218022105.25\tPASS\t-\tframeshift_variant\tPKD1L2\tENSG00000166473" />
+                        <has_text_matching expression="16\t81242198\trs7499011\tG\tA\t124146106.95\tPASS\tA\tstop_gained\tPKD1L2\tENSG00000166473" />
+                        <has_text_matching expression="3\t130114290\trs115380050\tC\tT\t105366.23\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" />
+                        <has_text_matching expression="3\t130139996\trs139339125\tG\tT\t576280.08\tPASS\tT\tsplice_acceptor_variant\tCOL6A5\tENSG00000172752" />
+                        <has_text_matching expression="3\t130159309\t.\tAAT\tA\t3284.41\tPASS\t-\tframeshift_variant\tCOL6A5\tENSG00000172752" />
+                        <has_text_matching expression="3\t130159330\trs2201717\tC\tT\t8770317.31\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" />
+                        <has_text_matching expression="3\t130187662\trs115375867\tG\tT\t1785133.61\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" />
+                        <has_text_matching expression="3\t130190720\trs11355796\tAT\tA\t157372019.43\tPASS\t-\tframeshift_variant\tCOL6A5\tENSG00000172752" />
+                        <has_text_matching expression="3\t53324819\trs782498227\tATGGCAC\tA\t304085671.95\tPASS\t-\tsplice_donor_variant&amp;intron_variant\tDCP1A\tENSG00000162290" />
+                        <has_text_matching expression="3\t46414935\trs938517991\tAT\tA\t9974.16\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
+                        <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t74264261.52\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
+                        <has_text_matching expression="3\t46415066\trs146972949\tC\tT\t120238.89\tPASS\tT\tstop_gained\tCCR5\tENSG00000160791" />
+                        <has_text_matching expression="16\t81242148\trs752607955\tGTT\tG\t12370921.18\tPASS\t-\tframeshift_variant\tPKD1L2\tENSG00000166473" />
+                        <has_text_matching expression="16\t81242198\trs7499011\tG\tA\t7423817.85\tPASS\tA\tstop_gained\tPKD1L2\tENSG00000166473" />
+                        <has_text_matching expression="17\t38975327\trs764791942\tT\tTAGCCGCCGCC\t282793.87\tPASS\tAGCCGCCGCC\tframeshift_variant\tKRT10\tENSG00000186395" />
+                        <has_text_matching expression="17\t38975329\trs762667965\tG\tGAGCTT\t238711.24\tPASS\tAGCTT\tframeshift_variant\tKRT10\tENSG00000186395" />
+                        <has_text_matching expression="3\t130159330\trs2201717\tC\tT\t165579.83\tPASS\tT\tstop_gained\tCOL6A5\tENSG00000172752" />
+                        <has_text_matching expression="3\t130190720\trs11355796\tAT\tA\t14066881.99\tPASS\t-\tframeshift_variant\tCOL6A5\tENSG00000172752" />
+                        <has_text_matching expression="3\t53324819\trs782498227\tATGGCAC\tA\t17202744.04\tPASS\t-\tsplice_donor_variant&amp;intron_variant\tDCP1A\tENSG00000162290" />
+                        <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t1947603.90\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
+                    </assert_contents>
+                </output>
+        </test>
     </tests>
     <help><![CDATA[
 
@@ -75,3 +118,4 @@
     }</citation>
     </citations>
 </tool>
+
diff -r 3bfa1089a2c4 -r 49012f2b4c19 test-data/patch-results/Nonessential_Host_Genes_(Basic).txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/patch-results/Nonessential_Host_Genes_(Basic).txt	Mon Apr 20 17:04:56 2020 -0400
@@ -0,0 +1,7 @@
+RPEL1
+OTOGL
+PKD1L2
+COL6A5
+DCP1A
+CCR5
+KRT10
diff -r 3bfa1089a2c4 -r 49012f2b4c19 test-data/patch-results/Nonessential_Host_Genes_(Detailed).txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/patch-results/Nonessential_Host_Genes_(Detailed).txt	Mon Apr 20 17:04:56 2020 -0400
@@ -0,0 +1,23 @@
+Chromosome	Position_Start	RSID	Reference_Allele	Alternate_Allele	Score	Quality	LoF_Variant	LoF_Annotation	HGNC_Symbol	Ensembl Code
+10	105005931	rs61746130	C	T	4480914.72	PASS	T	stop_gained	RPEL1	ENSG00000235376
+12	80770908	rs1222716200	C	T	4175.99	PASS	T	stop_gained	OTOGL	ENSG00000165899
+16	81242148	rs752607955	GTT	G	218022105.25	PASS	-	frameshift_variant	PKD1L2	ENSG00000166473
+16	81242198	rs7499011	G	A	124146106.95	PASS	A	stop_gained	PKD1L2	ENSG00000166473
+3	130114290	rs115380050	C	T	105366.23	PASS	T	stop_gained	COL6A5	ENSG00000172752
+3	130139996	rs139339125	G	T	576280.08	PASS	T	splice_acceptor_variant	COL6A5	ENSG00000172752
+3	130159309	.	AAT	A	3284.41	PASS	-	frameshift_variant	COL6A5	ENSG00000172752
+3	130159330	rs2201717	C	T	8770317.31	PASS	T	stop_gained	COL6A5	ENSG00000172752
+3	130187662	rs115375867	G	T	1785133.61	PASS	T	stop_gained	COL6A5	ENSG00000172752
+3	130190720	rs11355796	AT	A	157372019.43	PASS	-	frameshift_variant	COL6A5	ENSG00000172752
+3	53324819	rs782498227	ATGGCAC	A	304085671.95	PASS	-	splice_donor_variant&intron_variant	DCP1A	ENSG00000162290
+3	46414935	rs938517991	AT	A	9974.16	PASS	-	frameshift_variant	CCR5	ENSG00000160791
+3	46414943	rs775750898	TACAGTCAGTATCAATTCTGGAAGAATTTCCAG	T	74264261.52	PASS	-	frameshift_variant	CCR5	ENSG00000160791
+3	46415066	rs146972949	C	T	120238.89	PASS	T	stop_gained	CCR5	ENSG00000160791
+16	81242148	rs752607955	GTT	G	12370921.18	PASS	-	frameshift_variant	PKD1L2	ENSG00000166473
+16	81242198	rs7499011	G	A	7423817.85	PASS	A	stop_gained	PKD1L2	ENSG00000166473
+17	38975327	rs764791942	T	TAGCCGCCGCC	282793.87	PASS	AGCCGCCGCC	frameshift_variant	KRT10	ENSG00000186395
+17	38975329	rs762667965	G	GAGCTT	238711.24	PASS	AGCTT	frameshift_variant	KRT10	ENSG00000186395
+3	130159330	rs2201717	C	T	165579.83	PASS	T	stop_gained	COL6A5	ENSG00000172752
+3	130190720	rs11355796	AT	A	14066881.99	PASS	-	frameshift_variant	COL6A5	ENSG00000172752
+3	53324819	rs782498227	ATGGCAC	A	17202744.04	PASS	-	splice_donor_variant&intron_variant	DCP1A	ENSG00000162290
+3	46414943	rs775750898	TACAGTCAGTATCAATTCTGGAAGAATTTCCAG	T	1947603.90	PASS	-	frameshift_variant	CCR5	ENSG00000160791
diff -r 3bfa1089a2c4 -r 49012f2b4c19 test-data/patch.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/patch.txt	Mon Apr 20 17:04:56 2020 -0400
@@ -0,0 +1,48 @@
+CD4
+ALCAM
+TPST2
+CCR5
+SLC35B2
+PRM3
+TPBGL
+PCDHB9
+FMN1
+SEC22B
+COL6A5
+ANKRD63
+ITIH5
+PPP2R2D
+DNAJC5B
+FAT3
+WNK2
+FER1L5
+SEMA3B
+FIGNL2
+NUTM2B
+AGAP11
+TSGA10IP
+DNAH17
+ENO4
+KRT10
+C6orf229
+HNRNPCP5
+SLC22A31
+MYCBP2
+OTOGL
+ST8SIA1
+PKD1L2
+PIGB
+ZSCAN26
+CASP8AP2
+CCDC168
+HEATR5A
+NEURL3
+SLC35F4
+COPG2
+DCP1A
+DOC2B
+FOXD1
+FTH1P18
+RHBG
+RPEL1
+TLX1NB