Mercurial > repos > dereeper > plink

diff plink.xml @ 8:f733bf4f49ca draft default tip

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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 08:58:55 -0400
parents d6a7be1b5adb
children
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line diff
--- a/plink.xml	Wed Feb 07 00:16:59 2018 -0500
+++ b/plink.xml	Mon Apr 16 08:58:55 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="sniplay_plink" name="plink" version="1.0">
+<tool id="sniplay_plink" name="PLINK" version="2.0.0">
     
     <!-- [REQUIRED] Tool description displayed after the tool name -->
-    <description> - Filter large VCF file</description>
+    <description>Filter large VCF file</description>
     
     <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
     <requirements>
@@ -53,13 +53,13 @@
     
     <!-- [REQUIRED] Output files -->
     <outputs>
-	<data name="fileout" format="vcf" label="Plink filtered VCF"/>
-	<data name="filelog" format="txt" label="Plink logfile" />
+	<data name="fileout" format="vcf" label="PLINK filtered VCF"/>
+	<data name="filelog" format="txt" label="PLINK logfile" />
     </outputs>
     
     <tests>
         <test>
-            <param name="vcf" value="input.vcf"/>
+            <param name="vcf" value="plink_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"/>
@@ -68,31 +68,57 @@
             <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"/>
+            <output name="fileout" file="plink_output.vcf" compare="diff" lines_diff="2"/>
         </test>
     </tests> 
     
     <!-- [OPTIONAL] Help displayed in Galaxy -->
-    <help>
+    <help><![CDATA[
 
 .. class:: infomark
 
-**Authors**     Shaun Purcell : plink_
-
-.. _plink: https://www.cog-genomics.org/plink2
+**Authors**  Shaun Purcell : https://www.cog-genomics.org/plink2
 
  | **Please cite** "PLINK: a toolset for whole-genome association and population-based linkage analysis.", Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC, **American Journal of Human Genetics**, 2007 
 
 .. class:: infomark
 
-**Galaxy integration** Dereeper Alexis (IRD), Andres Gwendoline (Institut Français de Bioinformatique).
+**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
 
 .. class:: infomark
 
-**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
+**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
+
+---------------------------------------------------
+
+=====
+PLINK
+=====
 
+-----------
+Description
+-----------
 
+  | Genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.  
+  | For further informations, please visit the plink website_.
+
+.. _website: https://www.cog-genomics.org/plink2
 
-    </help>
+------------
+Dependencies
+------------
+
+PLINK
+        plink_ 1.90b4, Conda version
+Bioperl
+        perl-bioperl_ 1.6.924, Conda version
 
+.. _plink: https://anaconda.org/bioconda/plink
+.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
+
+    ]]></help>
+    <citations>
+       <citation type="doi">10.1086/519795</citation>
+       <citation type="doi">10.1186/s13742-015-0047-8</citation>
+    </citations>
 </tool>