# HG changeset patch # User Lance Parsons # Date 1348263640 14400 # Node ID 2861eb44fbbfd1b485c7fa57f39c900d9cd225d0 # Parent 8a5d43b21c6e4c8e62c88de5ed29dbf2c688d4f7 Fix issue with workflows (type->featuretype) and general error check diff -r 8a5d43b21c6e -r 2861eb44fbbf htseq-count.xml --- a/htseq-count.xml Thu Sep 20 12:41:53 2012 -0400 +++ b/htseq-count.xml Fri Sep 21 17:40:40 2012 -0400 @@ -25,7 +25,7 @@ --mode=$mode --stranded=$stranded --minaqual=$minaqual - --type=$type + --type=$featuretype --idattr=$idattr #if $samout_conditional.samout: --samout=$__new_file_path__/${samoutfile.id}_tmp @@ -42,7 +42,7 @@ #end if - Paired-End data MUST be sorted by QUERY NAME, use Picard Read Mate Fixer and Query name sort order before using this tool on paired data + Paired-End data MUST be sorted by QUERY NAME, use "NGS: Picard - Paired Read Mate Fixer" to sort by QUERY NAME and output to SAM (not BAM) before using this tool on paired data. @@ -60,7 +60,7 @@ Skip all reads with alignment quality lower than the given minimum value - + Feature type (3rd column in GFF file) to be used. All features of other types are ignored. The default, suitable for RNA-Seq and Ensembl GTF files, is exon. @@ -106,6 +106,7 @@ +