Mercurial > repos > iuc > stringtie
comparison stringtie.xml @ 20:48258a274be2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 57441e46de7ca04f25df6e43152dc210d4b32712
| author | iuc |
|---|---|
| date | Fri, 04 May 2018 08:37:21 -0400 |
| parents | 0c85a528a771 |
| children | f4e465352f50 |
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| 19:0c85a528a771 | 20:48258a274be2 |
|---|---|
| 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"/> |