Mercurial > repos > bebatut > humann2
changeset 19:8192fbe69c0e 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 06:18:29 -0500 |
| parents | 2caada2d49bc |
| children | a8d89b78b6e2 |
| files | humann2.xml repository_dependencies.xml |
| diffstat | 2 files changed, 7 insertions(+), 6 deletions(-) [+] |
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--- a/humann2.xml Thu Mar 02 09:25:07 2017 -0500 +++ b/humann2.xml Fri Mar 03 06:18:29 2017 -0500 @@ -67,9 +67,10 @@ #set $metaphlan_option += " --bowtie2db " + ref_db/ref_db #set $metaphlan_option += " --mpa_pkl " + ref_db/metadata.pkl #else - #set $path = $db.cached_db.fields.path - --bowtie2db `ls $path/*.pkl | sed 's/\(.*\)\..*/\1/'` - --mpa_pkl `ls $path/*.pkl` + #set $path = $taxo_profile.metaphlan2_db_choice.cached_db.fields.path + #set $value = $taxo_profile.metaphlan2_db_choice.cached_db.fields.value + --bowtie2db $path/$value + --mpa_pkl $path/$value'.pkl' #end if #end if --metaphlan-options="$metaphlan_option" @@ -182,8 +183,8 @@ </conditional> <param name="id_mapping" argument="--id-mapping" type="data" format="tsv" label="id mapping file for alignments" optional="True"/> <param name='translated_alignment' argument="--translated-alignment" type="select" label="Software to use for translated alignment" help="(--pathways)"> - <option value="rapsearch" selected="true">Rapsearch</option> - <option value="diamond">Diamond</option> + <option value="rapsearch">Rapsearch</option> + <option value="diamond" selected="true">Diamond</option> </param> <param argument='--xipe' type='boolean' checked="false" truevalue='on' falsevalue='off' label="Use xipe computation?"/> <param argument='--minpath' type='boolean' checked="true" truevalue='on' falsevalue='off' label="Use minpath computation?"/>
--- a/repository_dependencies.xml Thu Mar 02 09:25:07 2017 -0500 +++ b/repository_dependencies.xml Fri Mar 03 06:18:29 2017 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> <repositories description="This requires the HUMAnN2 data manager definition to install all required databases."> - <repository changeset_revision="8602983cb86f" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="bf858d6f7365" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="a0eed08a6b61" name="data_manager_humann2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>