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comparison htseq-count.xml @ 13:256d3114ce31

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Fix input format string and change dependency owners to devteam
author lparsons
date Fri, 11 Apr 2014 13:58:07 -0400
parents c86659f03e98
children c1db55359a86
comparison
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12:c86659f03e98 13:256d3114ce31
33 | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}' > $counts 2>$othercounts 33 | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}' > $counts 2>$othercounts
34 #if $samout_conditional.samout: 34 #if $samout_conditional.samout:
35 && samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile 35 && samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile
36 #end if</command> 36 #end if</command>
37 <inputs> 37 <inputs>
38 <param format="sam, bam" name="samfile" type="data" label="Aligned SAM/BAM File"/> 38 <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
39 <param format="gff" name="gfffile" type="data" label="GFF File"/> 39 <param format="gff" name="gfffile" type="data" label="GFF File"/>
40 <param name="mode" type="select" label="Mode"> 40 <param name="mode" type="select" label="Mode">
41 <help>Mode to handle reads overlapping more than one feature.</help> 41 <help>Mode to handle reads overlapping more than one feature.</help>
42 <option value="union" selected="true">Union</option> 42 <option value="union" selected="true">Union</option>
43 <option value="intersection-strict">Intersection (strict)</option> 43 <option value="intersection-strict">Intersection (strict)</option>