Mercurial > repos > yhoogstrate > featurecounts
comparison featurecounts.xml @ 10:3250ee31bdbb draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318
| author | yhoogstrate |
|---|---|
| date | Mon, 18 May 2015 04:45:52 -0400 |
| parents | c74b27b17d73 |
| children | 0eea16542649 |
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| 9:c74b27b17d73 | 10:3250ee31bdbb |
|---|---|
| 62 ${alignment} | 62 ${alignment} |
| 63 #end for | 63 #end for |
| 64 | 64 |
| 65 2>&1 | 65 2>&1 |
| 66 | 66 |
| 67 #set $columns = [str(i+7) for i, alignment in enumerate($alignments)] | 67 #set $columns = [str(i+7) for i, alignment in enumerate($alignments)] |
| 68 #set $columns=",".join($columns) | 68 #set $columns=",".join($columns) |
| 69 | |
| 69 #if $format == "tabdel_default" or $format.value == "tabdel_default" | 70 #if $format == "tabdel_default" or $format.value == "tabdel_default" |
| 70 ; cp $output tmp.txt | 71 ; cp $output tmp.txt |
| 71 ; egrep -v "^#" tmp.txt > tmp2.txt | 72 ; egrep -v "^#" tmp.txt > tmp2.txt |
| 72 ; cut -f 1,$columns tmp2.txt > tmp_left.txt | 73 ; cut -f 1,$columns tmp2.txt > tmp_left.txt |
| 73 ; cut -f 6 tmp2.txt > tmp_right.txt | 74 ; cut -f 6 tmp2.txt > tmp_right.txt |
| 193 | 194 |
| 194 <outputs> | 195 <outputs> |
| 195 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> | 196 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> |
| 196 <data format="tabular" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" /> | 197 <data format="tabular" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" /> |
| 197 </outputs> | 198 </outputs> |
| 198 | 199 |
| 199 <tests> | 200 <tests> |
| 200 <test> | 201 <test> |
| 201 <param name="alignments" value="featureCounts_input1.bam,featureCounts_input2.bam" ftype="bam" /> | 202 <param name="alignments" value="featureCounts_input1.bam,featureCounts_input2.bam" ftype="bam" /> |
| 202 <param name="source_select" value="history" /> | 203 <param name="source_select" value="history" /> |
| 203 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> | 204 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> |
| 204 <output name="output" file="output.tab"/> | 205 <output name="output" file="output.tab"/> |
| 205 <output name="output_summary" file="output_summary.tab"/> | 206 <output name="output_summary" file="output_summary.tab"/> |
| 206 </test> | 207 </test> |
| 207 </tests> | 208 </tests> |
| 209 | |
| 208 <help> | 210 <help> |
| 209 featureCounts | 211 featureCounts |
| 210 ############# | 212 ############# |
| 211 | 213 |
| 212 Overview | 214 Overview |