Mercurial > repos > devteam > picard
diff picard_AddOrReplaceReadGroups.xml @ 8:3a3234d7a2e8 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
| author | devteam |
|---|---|
| date | Thu, 16 Jul 2015 15:53:10 -0400 |
| parents | 3d4f1fa26f0e |
| children | 05087b27692a |
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--- a/picard_AddOrReplaceReadGroups.xml Thu Jan 29 16:11:15 2015 -0500 +++ b/picard_AddOrReplaceReadGroups.xml Thu Jul 16 15:53:10 2015 -0400 @@ -1,40 +1,26 @@ -<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="1.126.0"> +<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.0"> <description>add or replaces read group information</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> + <import>read_group_macros.xml</import> </macros> - + <expand macro="requirements" /> <command> + @define_read_group_helpers@ + #set $rg_auto_name = $read_group_name_default($inputFile) + @set_read_group_vars@ @java_options@ java -jar \$JAVA_JAR_PATH/picard.jar AddOrReplaceReadGroups INPUT="${inputFile}" - RGLB="${rglb}" - RGPL="${rgpl}" - RGPU="${rgpu}" - RGSM="${rgsm}" - RGID="${rgid}" - - #if str( $rgcn): - RGCN="${rgcn}" - #end if - - #if str( $rgds): - RGDS="${rgds}" - #end if - - #if str( $rgpi): - RGPI="${rgpi}" - #end if - - #if str( $rgdt): - RGDT="${rgdt}" - #end if - + $format_read_group("RGLB=", $rg_lb, '"') + $format_read_group("RGPL=", $rg_pl, '"') + $format_read_group("RGPU=", $rg_pu, '"') + $format_read_group("RGSM=", $rg_sm, '"') + $format_read_group("RGID=", $rg_id, '"') + $format_read_group("RGDS=", $rg_ds, '"') + $format_read_group("RGPI=", $rg_pi, '"') + $format_read_group("RGDT=", $rg_dt, '"') VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR @@ -44,17 +30,7 @@ <inputs> <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> - <param name="rgid" value="A" type="text" label="Read Group ID" help="RGID; Required" /> - <param name="rgsm" value="sample-a" type="text" label="Read Group Sample name" help="RGSM; Required" /> - <param name="rglb" value="tumor-a" type="text" label="Read Group library" help="RGLB; Required" /> - <param name="rgpl" value="Illumina" type="text" label="Read Group Platform" help="RGPL; Required; e.g., Illumina, 454, IonTorrent, etc" /> - <param name="rgpu" value="run-1" type="text" label="Read Group Platform Unit" help="RGPU; Required; e.g., run, barcode, etc" /> - <!-- optional params --> - <param name="rgcn" value="" optional="True" type="text" label="Read Group sequencing center name" help="RGCN; Optional" /> - <param name="rgds" value="" optional="True" type="text" label="Read Group description" help="RGDS; Optional" /> - <param name="rgpi" value="" optional="True" type="integer" label="Read Group predicted insert size" help="RGPI; Optional" /> - <param name="rgdt" value="" optional="True" type="text" label="Read Group run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/> - + <expand macro="read_group_inputs_picard" /> <expand macro="VS" /> </inputs> @@ -70,11 +46,11 @@ <tests> <test> <param name="inputFile" value="picard_ARRG.bam" /> - <param name="rglb" value="tumor-a" /> - <param name="rgpl" value="Illumina" /> - <param name="rgpu" value="run-1" /> - <param name="rgsm" value="sample-a" /> - <param name="rgid" value="id-1" /> + <param name="LB" value="tumor-a" /> + <param name="PL" value="ILLUMINA" /> + <param name="PU" value="run-1" /> + <param name="SM" value="sample-a" /> + <param name="ID" value="id-1" /> <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" /> </test> </tests> @@ -146,3 +122,4 @@ +