Mercurial > repos > iuc > multiqc
comparison multiqc.xml @ 3:f2a3895ba15a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4a9e5506db1a6b93486b617162e1b59abcdd0f1b
| author | iuc |
|---|---|
| date | Fri, 17 Nov 2017 13:27:05 -0500 |
| parents | 39f063be9fb4 |
| children | e4574a4d09d8 |
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| 2:39f063be9fb4 | 3:f2a3895ba15a |
|---|---|
| 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" |