diff plink.xml @ 7:d6a7be1b5adb draft

Uploaded

--- a/plink.xml	Wed Feb 07 00:15:42 2018 -0500
+++ b/plink.xml	Wed Feb 07 00:16:59 2018 -0500
@@ -6,9 +6,11 @@
     <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
     <requirements>
         <requirement type="binary">perl</requirement>
+        <requirement type="package" version="1.6.924">perl-bioperl</requirement>
 	<requirement type="package" version="1.90b4">plink</requirement>
     </requirements>
     
+    <code file="find_indiv.py"/>
 
     <!-- [STRONGLY RECOMMANDED] Exit code rules -->
     <stdio>
@@ -30,7 +32,6 @@
 	$chromosomes
 	#end if
     </command>
-    <code file="find_indiv.py"/>
     <!-- [REQUIRED] Input files and tool parameters -->
     <inputs>
 	<param name="vcf" type="data" format="vcf" optional="false" label="VCF input" />
@@ -56,6 +57,20 @@
 	<data name="filelog" format="txt" label="Plink logfile" />
     </outputs>
     
+    <tests>
+        <test>
+            <param name="vcf" value="input.vcf"/>
+            <param name="samples" value="AZUCENA,BULUPANDAK,GIZA171,IAC165,KHAODAM,M202,MOROBEREKAN,NIPPONBARE.D,62667,63-104,ARAGUAIA,ARIAS,ARROZCEBADA,BABER,BAGANANASALAO,BAKUNGH,BENGALYVAKARINA,BICOBRANCO,BINULAWAN,CAIAPO,CANAROXA,CANELADEFERRO,CHALOYOE,CHAPHUMA,CICIHBETON,CIRAD358,CIRAD392,CIRAD394,CIRAD403,CIRAD409,CIRAD488,CNA-7.BO.1.1.33-13-6-1,COLOMBIA1,CT13582-15-5-M,CUBA65,CUIABANA,CURINCA,DAM,DANGREY,DAVAO,DAWASANRED,DINORADO,DOURADOAGULHA,DOURADOPRECOCE,ESPERANZA,FOHISOMOTRA,GANIGI,GEMJYAJYANAM,GOGO,GOGOLEMPUK,GOGOLEMPAK,GOMPA2,GRAZI,GUARANI,GUNDILKUNING,HAWMOM,HD1-4,IAC25,IAC47,IDSA77,IGUAPECATETO,INDANE,IR60080-46A,IR63380-16,IR63372-08,IR65907-188-1-B,IR66421-096-2-1-1,IR68704-145-1-1-B,IR71525-19-1-1,IRAT104,IRAT109,IRAT112,IRAT13,IRAT144,IRAT170,IRAT177,IRAT2,IRAT212,IRAT216,IRAT234,IRAT257,IRAT335,IRAT362,IRAT364,IRAT366,IRAT380,JAOHAW,JIMBRUKJOLOWORO,JUMALI,JUMULA2,KAKANI2,KANIRANGA,KARASUKARASURANKASU,KEDAYAN,KENDINGA5H,KETANKONIR,KETANLUMBU,KETANMENAH,KHAOKAPXANG,KINANDANGPATONG,KOMOJAMANITRA,KU115,KUROKA,LAMBAYQUE1,LUDAN,MAHAE,MAINTIMOLOTSY1226,MALAGKITPIRURUTONG,MANANELATRA520,MANDRIRAVINA3512,MARAVILHA,MITSANGANAHIJERY,MOLOK,NABESHI,NEPHOAVANG,NHTA10,NHTA5,NPE253,NPE826,ORYZICASABANA6,OS4,OS6,P5589-1-1-3-P,PACHOLINHA,PADIBOENAR,PADIKASALLE,PALAWAN,PATEBLANCMAN1,PCT11.0.0.2.BO.1.55-1-3-1,PCT4.SA.4.1.1076-2-4-1-5,PEHPINUO,POENOETHITAM,PULULAPA,RATHAL,REKETMAUN,RT1031-69,SENG,SPEAKER,TANDUI,TREMBESE,TRESMESES,TSIPALA89,VARYLAVA90,VARYLAVADEBETAFO,VARYMADINIKA3566,VARYMALADY,VARYSOMOTRASIHANAKA,WAB56-125,WAB56-50,WAB706-3-4-K4-KB-1,YANCAOUSSA,YANGKUMRED,YUNLU7,IR47686-09-01-B-1,IR53236-275-1,IR65261-19-1-B,IR65907-206-4-B,IR66421-105-1-1,IR71524-44-1-1,VIETNAM1,VIETNAM3,IR47684-05-1-B,PRIMAVERA,CHUAN3,CHUAN4,EARLYMUTANTIAC165"/>
+            <param name="frequency" value="0"/>
+            <param name="max_freq" value="0.5"/>
+            <param name="allow_missing" value="1"/>
+            <param name="type_p" value="ALL"/>
+            <param name="chromosomes" value=""/>
+            <param name="bound_start" value="1"/>
+            <param name="bound_end" value="100000000"/>
+            <output name="fileout" file="output.vcf" compare="diff" lines_diff="2"/>
+        </test>
+    </tests> 
     
     <!-- [OPTIONAL] Help displayed in Galaxy -->
     <help>