Mercurial > repos > bebatut > humann2
changeset 22:56e8ce2f3c96 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f45f31529390153bdaf93a3c94a65f6888ed484b\n'-dirty
author | bebatut |
---|---|
date | Fri, 03 Mar 2017 06:51:09 -0500 |
parents | 8b86d590b442 |
children | 928ad2c3e0c2 |
files | README.rst humann2.xml |
diffstat | 2 files changed, 11 insertions(+), 13 deletions(-) [+] |
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--- a/README.rst Fri Mar 03 06:40:48 2017 -0500 +++ b/README.rst Fri Mar 03 06:51:09 2017 -0500 @@ -4,11 +4,9 @@ Galaxy should be able to automatically install the dependencies, i.e. the HUMAnN2 binaries and its dependencies. -After installation, you must tell Galaxy about the defaut database with -clade-specific marker genes used for taxonomic profiling (MetaPhlAn2), and where -to find it: +After installation, you must tell Galaxy about the defaut databases for MetaPhlAn2 and HUMAnN2. +You need to use the data managers for that and installing: -* Put the ``metaphlan2_db.loc`` file in the ``tool-data/`` folder, after uncommenting last line -* Download whole MetaPhlan2 source code: https://bitbucket.org/biobakery/metaphlan2/get/2.5.0.zip -* Unzip it -* Move ``db_v20`` folder into ``dependency_dir/metaphlan2/2.5.0/bebatut/package_metaphlan2_2_5_0/...`` folder +- MetaPhlAn2 database +- HUMAnN2 nucleotide database +- HUMAnN2 protein database \ No newline at end of file
--- a/humann2.xml Fri Mar 03 06:40:48 2017 -0500 +++ b/humann2.xml Fri Mar 03 06:51:09 2017 -0500 @@ -59,21 +59,21 @@ $bypass_nucleotide_search --annotation-gene-index $annotation_gene_index - #set $metaphlan_option = '-t rel_ab' + #set $metaphlan_option = "-t rel_ab" #if $taxo_profile.taxonomic_profile_test == "true": --taxonomic-profile '$taxo_profile.taxonomic_profile' #else #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history" - #set $metaphlan_option += ' --bowtie2db ' + ref_db/ref_db - #set $metaphlan_option += ' --mpa_pkl ' + ref_db/metadata.pkl + #set $metaphlan_option += " --bowtie2db " + ref_db/ref_db + #set $metaphlan_option += " --mpa_pkl " + ref_db/metadata.pkl #else #set $path = $taxo_profile.metaphlan2_db_choice.cached_db.fields.path #set $value = $taxo_profile.metaphlan2_db_choice.cached_db.fields.value - #set $metaphlan_option += ' --bowtie2db ' + $path/$value - #set $metaphlan_option += ' --mpa_pkl ' + $path/$value + '.pkl' + #set $metaphlan_option += " --bowtie2db " + $path/$value + #set $metaphlan_option += " --mpa_pkl " + $path/$value + ".pkl" #end if #end if - --metaphlan-options='$metaphlan_option' + --metaphlan-options="$metaphlan_option" #if $nucleotide_db.nucleotide_db_selector == "cached" --nucleotide-database '$nucleotide_db.nucleotide_database.fields.path'