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comparison metaphlan2.xml @ 2:5b7ee956d89b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
author iuc
date Fri, 19 Mar 2021 09:36:09 +0000
parents f279fc0892fc
children f23f49426a3c
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1:f279fc0892fc 2:5b7ee956d89b
1 <tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.0"> 1 <tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.1">
2 2
3 <description>to profile the composition of microbial communities</description> 3 <description>to profile the composition of microbial communities</description>
4 4
5 <macros> 5 <macros>
6 <import>metaphlan2_macros.xml</import> 6 <import>metaphlan2_macros.xml</import>
25 --json_input '$db.mpa_pkl' 25 --json_input '$db.mpa_pkl'
26 --pkl_output 'ref_db/metadata.pkl' 26 --pkl_output 'ref_db/metadata.pkl'
27 && 27 &&
28 #end if 28 #end if
29 29
30 #if $input_file.datatype.file_ext.startswith("fastq")
31 #set ext='fastq'
32 #else
33 #set ext=$input_file.datatype.file_ext
34 #end if
35
30 metaphlan2.py 36 metaphlan2.py
31 '$input_file' 37 '$input_file'
32 -o '$output_file' 38 -o '$output_file'
33 --input_type '${input_file.datatype.file_ext}' 39 --input_type $ext
34 --bowtie2_exe `which bowtie2` 40 --bowtie2_exe `which bowtie2`
35 41
36 #if $db.db_selector == "cached" 42 #if $db.db_selector == "cached"
37 #set $path = $db.cached_db.fields.path 43 #set $path = $db.cached_db.fields.path
38 #set $value = $db.cached_db.fields.value 44 #set $value = $db.cached_db.fields.value