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comparison stringtie.xml @ 14:eafd5dc95228 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 57441e46de7ca04f25df6e43152dc210d4b32712
author iuc
date Fri, 04 May 2018 08:37:37 -0400
parents a305d75e13f2
children dd4df992d93d
comparison
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13:a305d75e13f2 14:eafd5dc95228
101 && 101 &&
102 head -n 1 transcript_counts.csv | sed -e 's/sample1/$escaped_element_identifier/' > '$transcript_counts' 102 head -n 1 transcript_counts.csv | sed -e 's/sample1/$escaped_element_identifier/' > '$transcript_counts'
103 #end if 103 #end if
104 ## Sort count files on the first column 104 ## Sort count files on the first column
105 && 105 &&
106 tail -n +2 gene_counts.csv | sort -t"\${TAB}" -k1 >> '$gene_counts' 106 tail -n +2 gene_counts.csv | sort -t"\${TAB}" -k1,1 >> '$gene_counts'
107 && 107 &&
108 tail -n +2 transcript_counts.csv | sort -t"\${TAB}" -k1 >> '$transcript_counts' 108 tail -n +2 transcript_counts.csv | sort -t"\${TAB}" -k1,1 >> '$transcript_counts'
109 #end if 109 #end if
110 #end if 110 #end if
111 ]]></command> 111 ]]></command>
112 <inputs> 112 <inputs>
113 <param name="input_bam" type="data" format="sam,bam" label="Input mapped reads" help="Input BAM/SAM file containing reads you want to assemble into transcripts"/> 113 <param name="input_bam" type="data" format="sam,bam" label="Input mapped reads" help="Input BAM/SAM file containing reads you want to assemble into transcripts"/>