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comparison multiqc.xml @ 3:fb44dede6db8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4a9e5506db1a6b93486b617162e1b59abcdd0f1b
author iuc
date Fri, 17 Nov 2017 13:26:48 -0500
parents 2ae61e6168d4
children 08188e2202aa
comparison
equal deleted inserted replaced
2:2ae61e6168d4 3:fb44dede6db8
277 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) 277 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
278 #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) 278 #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j)
279 mkdir $repeat_dir && 279 mkdir $repeat_dir &&
280 #if str($repeat2.type.type) == "log" 280 #if str($repeat2.type.type) == "log"
281 #for $file in $repeat2.type.input 281 #for $file in $repeat2.type.input
282 ln -s '$file' '${repeat_dir}/{$file.element_identifier}_Log.final.out' && 282 ln -s '$file' '${repeat_dir}/${file.element_identifier}_Log.final.out' &&
283 #end for 283 #end for
284 #elif str($repeat2.type.type) == "genecounts" 284 #elif str($repeat2.type.type) == "genecounts"
285 #for $file in $repeat2.type.input 285 #for $file in $repeat2.type.input
286 ln -s '$file' '${repeat_dir}/{$file.element_identifier}_ReadsPerGene.out.tab' && 286 ln -s '$file' '${repeat_dir}/${file.element_identifier}_ReadsPerGene.out.tab' &&
287 #end for 287 #end for
288 #end if 288 #end if
289 #end for 289 #end for
290 #elif str($repeat.software_cond.software) == "tophat" 290 #elif str($repeat.software_cond.software) == "tophat"
291 #for $file in $repeat.software_cond.input 291 #for $file in $repeat.software_cond.input
298 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) 298 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
299 #set file_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) 299 #set file_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j)
300 mkdir $file_dir && 300 mkdir $file_dir &&
301 #if str($repeat2.type.type) == "relatedness2" 301 #if str($repeat2.type.type) == "relatedness2"
302 #for $file in $repeat2.type.input 302 #for $file in $repeat2.type.input
303 ln -s '$file' '${repeat_dir}/{$file.element_identifier}.relatedness2' && 303 ln -s '$file' '${repeat_dir}/${file.element_identifier}.relatedness2' &&
304 #end for 304 #end for
305 #elif str($repeat2.type) == "tstv_by_count" 305 #elif str($repeat2.type) == "tstv_by_count"
306 #for $file in $repeat2.type.input 306 #for $file in $repeat2.type.input
307 ln -s '$file' '${repeat_dir}/{$file.element_identifier}.TsTv.count' && 307 ln -s '$file' '${repeat_dir}/${file.element_identifier}.TsTv.count' &&
308 #end for 308 #end for
309 #elif str($repeat2.type) == "tstv_by_qual" 309 #elif str($repeat2.type) == "tstv_by_qual"
310 #for $file in $repeat2.type.input 310 #for $file in $repeat2.type.input
311 ln -s '$file' '${repeat_dir}/{$file.element_identifier}.TsTv.qual' && 311 ln -s '$file' '${repeat_dir}/${file.element_identifier}.TsTv.qual' &&
312 #end for 312 #end for
313 #elif str($repeat2.type) == "tstv_summary" 313 #elif str($repeat2.type) == "tstv_summary"
314 #for $file in $repeat2.type.input 314 #for $file in $repeat2.type.input
315 ln -s '$file' '${repeat_dir}/{$file.element_identifier}.TsTv.summary' && 315 ln -s '$file' '${repeat_dir}/${file.element_identifier}.TsTv.summary' &&
316 #end for 316 #end for
317 #end if 317 #end if
318 #end for 318 #end for
319 #else if str($repeat.software_cond.software) == "custom_content": 319 #else if str($repeat.software_cond.software) == "custom_content":
320 #set $configfile = "T" 320 #set $configfile = "T"