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comparison metaphlan2.xml @ 36:969ae2fd4c84 draft

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Uploaded
author bebatut
date Thu, 23 Feb 2017 08:00:20 -0500
parents c312685a4b26
children e7ed163633e1
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35:c312685a4b26 36:969ae2fd4c84
40 -o '$output_file' 40 -o '$output_file'
41 --input_type '${input_file.datatype.file_ext}' 41 --input_type '${input_file.datatype.file_ext}'
42 --bowtie2_exe `which bowtie2` 42 --bowtie2_exe `which bowtie2`
43 43
44 #if $db.db_selector == "cached" 44 #if $db.db_selector == "cached"
45 #set $paths = dict([(_[0], _[3]) for _ in $db.cached_db.input.options.tool_data_table.data]) 45 #set $path = ${db.cached_db.fields.path}
46 #set $db_choice = $db.cached_db.value 46 --bowtie2db `ls $path/*.pkl | sed 's/\(.*\)\..*/\1/'`
47 --bowtie2db `ls $paths[$db_choice]/*.pkl | sed 's/\(.*\)\..*/\1/'` 47 --mpa_pkl `ls $path/*.pkl`
48 --mpa_pkl `ls $paths[$db_choice]/*.pkl`
49 #else 48 #else
50 --bowtie2db 'ref_db/ref_db' 49 --bowtie2db 'ref_db/ref_db'
51 --mpa_pkl 'ref_db/metadata.pkl' 50 --mpa_pkl 'ref_db/metadata.pkl'
52 #end if 51 #end if
53 52
83 <option value="cached" selected="true">Locally cached</option> 82 <option value="cached" selected="true">Locally cached</option>
84 <option value="history">From history</option> 83 <option value="history">From history</option>
85 </param> 84 </param>
86 <when value="cached"> 85 <when value="cached">
87 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" > 86 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" >
88 <options from_data_table="metaphlan2_database" /> 87 <options from_data_table="metaphlan2_database" />
89 </param> 88 </param>
90 </when> 89 </when>
91 <when value="history"> 90 <when value="history">
92 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/> 91 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
93 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/> 92 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/>