Mercurial > repos > bgruening > deeptools
comparison deepTools_macros.xml @ 71:106cd88dc9da draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
| author | bgruening |
|---|---|
| date | Fri, 18 Sep 2015 07:34:39 -0400 |
| parents | a4bbac56f046 |
| children | c56a8c021315 |
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| 70:a4bbac56f046 | 71:106cd88dc9da |
|---|---|
| 196 label="Bam file" multiple="true" | 196 label="Bam file" multiple="true" |
| 197 help="The BAM file must be sorted."/> | 197 help="The BAM file must be sorted."/> |
| 198 </xml> | 198 </xml> |
| 199 | 199 |
| 200 <xml name="multiple_input_bigwigs"> | 200 <xml name="multiple_input_bigwigs"> |
| 201 <repeat name="input_files" title="BigWig files" min="2"> | 201 <param name="bigwigfile" type="data" format="bigwig" multiple="True" |
| 202 <param name="bigwigfile" type="data" format="bigwig" | 202 label="Bigwig file" |
| 203 label="Bigwig file" | 203 help="The Bigwig file must be sorted."/> |
| 204 help="The Bigwig file must be sorted."/> | |
| 205 <param name="label" type="text" size="30" optional="true" value="" | |
| 206 label="Label" | |
| 207 help="Label to use in the output. If not given the dataset name will be used instead."/> | |
| 208 </repeat> | |
| 209 </xml> | 204 </xml> |
| 210 | 205 |
| 211 <xml name="plotTitle"> | 206 <xml name="plotTitle"> |
| 212 <param name="plotTitle" type="text" value="" size="30" optional="True" | 207 <param name="plotTitle" type="text" value="" size="30" optional="True" |
| 213 label="Title of the plot" | 208 label="Title of the plot" |
| 214 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" /> | 209 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" /> |
| 215 </xml> | 210 </xml> |
| 216 | 211 |
| 217 <token name="@multiple_input_bams@"> | 212 <token name="@multiple_input_bams@"> |
| 218 #import tempfile | 213 <![CDATA[ |
| 219 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) | |
| 220 #set files=[] | 214 #set files=[] |
| 221 #set labels=[] | 215 #set labels=[] |
| 222 #for $i in $bamfiles: | 216 #for $counter, $bamfile in enumerate($bamfiles): |
| 223 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) | 217 ln -s "${bamfile}" "./${counter}.bam" && |
| 224 #set $temp_input_path = $temp_input_handle.name | 218 ln -s "${bamfile}" "./${counter}.bam.bai" && |
| 225 #silent $temp_input_handle.close() | 219 #silent $files.append('%s.bam' % $counter) |
| 226 #silent os.system("ln -s %s %s.bam" % (str($i), $temp_input_path)) | 220 #silent $labels.append("'%s'" % ($bamfile.name)) |
| 227 #silent os.system("ln -s %s %s.bam.bai" % (str($i.metadata.bam_index), $temp_input_path)) | |
| 228 #silent $files.append('%s.bam' % $temp_input_path) | |
| 229 | |
| 230 #silent $labels.append("\"%s\"" % ($i.name)) | |
| 231 #end for | 221 #end for |
| 222 ]]> | |
| 232 </token> | 223 </token> |
| 233 | 224 |
| 234 <token name="@multiple_input_bigwigs@"> | 225 <token name="@multiple_input_bigwigs@"> |
| 235 #import tempfile | 226 <![CDATA[ |
| 236 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) | |
| 237 #set files=[] | 227 #set files=[] |
| 238 #set labels=[] | 228 #set labels=[] |
| 239 #for $i in $input_files: | 229 #for $counter, $bigwig in enumerate($input_files): |
| 240 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) | 230 ln -s "${bigwig}" "${counter}.bw" && |
| 241 #set $temp_input_path = $temp_input_handle.name | 231 #silent $files.append('%s.bw' % $counter) |
| 242 #silent $temp_input_handle.close() | 232 #silent $labels.append("'%s'" % ($bigwig.name)) |
| 243 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path)) | |
| 244 #silent $files.append('%s.bw' % $temp_input_path) | |
| 245 | |
| 246 ##set $files += [str($i.bigwigfile)] | |
| 247 #if str($i.label.value) != "": | |
| 248 #set $labels += ["\"%s\"" % ($i.label.value)] | |
| 249 #else | |
| 250 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)] | |
| 251 #end if | |
| 252 #end for | 233 #end for |
| 234 ]]> | |
| 253 </token> | 235 </token> |
| 254 | 236 |
| 255 <xml name="reference_genome_source"> | 237 <xml name="reference_genome_source"> |
| 256 <conditional name="source"> | 238 <conditional name="source"> |
| 257 <param name="ref_source" type="select" label="Reference genome"> | 239 <param name="ref_source" type="select" label="Reference genome"> |