Mercurial > repos > bebatut > metaphlan2
comparison metaphlan2.xml @ 32:c941148c75c7 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 9e93b527d3cc9023467b1b285b068dac21b0727b-dirty
| author | bebatut |
|---|---|
| date | Wed, 22 Feb 2017 03:49:35 -0500 |
| parents | 83f06bee818c |
| children | e8206e14e889 |
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| 31:83f06bee818c | 32:c941148c75c7 |
|---|---|
| 41 --input_type '${input_file.datatype.file_ext}' | 41 --input_type '${input_file.datatype.file_ext}' |
| 42 | 42 |
| 43 --bowtie2_exe `which bowtie2` | 43 --bowtie2_exe `which bowtie2` |
| 44 | 44 |
| 45 #if $db.db_selector == "cached" | 45 #if $db.db_selector == "cached" |
| 46 #set $table = dict([(_[0], _[2]) for _ in $db.cached_db.input.options.tool_data_table.data]) | 46 #set $paths = dict([(_[0], _[3]) for _ in $db.cached_db.input.options.tool_data_table.data]) |
| 47 #set $db_choice = $db.cached_db.value | 47 #set $db_choice = $db.cached_db.value |
| 48 --bowtie2db '$table[$db_choice]' | 48 #set $metadata = `ls $paths[$db_choice]/*.pkl` |
| 49 --mpa_pkl $table[$db_choice]".pkl" | 49 --bowtie2db $metadata[:-4] |
| 50 --mpa_pkl '$metadata' | |
| 50 #else | 51 #else |
| 51 --bowtie2db 'ref_db/ref_db' | 52 --bowtie2db 'ref_db/ref_db' |
| 52 --mpa_pkl 'ref_db/metadata.pkl' | 53 --mpa_pkl 'ref_db/metadata.pkl' |
| 53 #end if | 54 #end if |
| 54 | 55 |