readgroups

galaxyproject · Mar 2, 2024 · 91958ff · 91958ff
1 parent d462e02
commit 91958ff
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Showing 2 changed files with 12 additions and 12 deletions.
diff --git a/tools/picard/picard_AddOrReplaceReadGroups.xml b/tools/picard/picard_AddOrReplaceReadGroups.xml
@@ -14,14 +14,14 @@
     @symlink_element_identifier@
     picard AddOrReplaceReadGroups
       --INPUT '$escaped_element_identifier'
-      $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, '"')
+      $format_read_group("", $rg_lb, quote='"', arg=" --RGLB ")
+      $format_read_group("", $rg_pl, quote='"', arg=" --RGPL ")
+      $format_read_group("", $rg_pu, quote='"', arg=" --RGPU ")
+      $format_read_group("", $rg_sm, quote='"', arg=" --RGSM ")
+      $format_read_group("", $rg_id, quote='"', arg=" --RGID ")
+      $format_read_group("", $rg_ds, quote='"', arg=" --RGDS ")
+      $format_read_group("", $rg_pi, quote='"', arg=" --RGPI ")
+      $format_read_group("", $rg_dt, quote='"', arg=" --RGDT ")
       --OUTPUT '${outFile}'
       --VALIDATION_STRINGENCY '${validation_stringency}'
       --QUIET true

diff --git a/tools/picard/picard_ReorderSam.xml b/tools/picard/picard_ReorderSam.xml
@@ -19,10 +19,10 @@
     #if str( $reference_source.reference_source_selector ) == "history":
 
       picard CreateSequenceDictionary
-      --REFERENCE='${ref_fasta}'
-      --OUTPUT='${picard_dict}'
-      --QUIET=true
-      --VERBOSITY=ERROR
+      --REFERENCE '${ref_fasta}'
+      --OUTPUT '${picard_dict}'
+      --QUIET true
+      --VERBOSITY ERROR
 
       &&