Mercurial > repos > devteam > picard
diff picard_SamToFastq.xml @ 2:9227b8c3093b
Updated command line format per dev team standards.
| author | devteam <devteam@galaxyproject.org> |
|---|---|
| date | Tue, 02 Apr 2013 09:42:36 -0400 |
| parents | 1cd7f3b42609 |
| children | 3d4f1fa26f0e |
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--- a/picard_SamToFastq.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/picard_SamToFastq.xml Tue Apr 02 09:42:36 2013 -0400 @@ -8,8 +8,8 @@ -jar "\$JAVA_JAR_PATH/SamToFastq.jar" INPUT="${input_sam}" VALIDATION_STRINGENCY="LENIENT" - RE_REVERSE=${re_reverse} - INCLUDE_NON_PF_READS=${include_non_pf_reads} + RE_REVERSE="${re_reverse}" + INCLUDE_NON_PF_READS="${include_non_pf_reads}" #if str( $clipping_attribute ): CLIPPING_ATTRIBUTE="${clipping_attribute}" #end if @@ -22,7 +22,7 @@ #if str( $read1_max_bases_to_write ): READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}" #end if - INCLUDE_NON_PRIMARY_ALIGNMENTS=${include_non_primary_alignments} + INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}" #if str( $output_per_read_group_selector ) == 'per_sam_file': ##OUTPUT_PER_RG=false @@ -54,7 +54,7 @@ #end if ' --read_group_file_1 "${output_fastq1}" - --new_files_path "${$__new_file_path__}" + --new_files_path "${__new_file_path__}" --file_id_1 "${output_fastq1.id}" #end if </command>