Mercurial > repos > bebatut > humann2
changeset 10:a749062bc435 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
author | bebatut |
---|---|
date | Tue, 12 Apr 2016 03:06:03 -0400 |
parents | 7d2be77d5b83 |
children | e504cd2410a6 |
files | humann2.xml tool-data/metaphlan2_bowtie_db.loc.sample tool-data/metaphlan2_metadata.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
diffstat | 5 files changed, 33 insertions(+), 5 deletions(-) [+] |
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--- a/humann2.xml Thu Mar 31 03:35:17 2016 -0400 +++ b/humann2.xml Tue Apr 12 03:06:03 2016 -0400 @@ -36,10 +36,12 @@ #set $db = $nucleotide_database.value --nucleotide-database $data_table[$db] - --metaphlan \${METAPHLAN2_DIR}/ - --metaphlan-options "-t rel_ab" - --bowtie2 \${PATH} - --diamond \${PATH} + #set $mpa_pkl_table = dict([(_[0], _[2]) for _ in $mpa_pkl.input.options.tool_data_table.data]) + #set $mpa_pkl_db = $mpa_pkl.value + + #set $bowtie2_table = dict([(_[0], _[2]) for _ in $bowtie2db.input.options.tool_data_table.data]) + #set $bowtie2_db = $bowtie2db.value + --metaphlan-options="-t rel_ab --mpa_pkl $mpa_pkl_table[$mpa_pkl_db] --bowtie2db $bowtie2_table[$bowtie2_db]" --threads \${GALAXY_SLOTS:-4} @@ -69,6 +71,14 @@ <when value="false" /> </conditional> + <param name="mpa_pkl" label="Metadata for MetaPhlAn2" type="select" > + <options from_data_table="metaphlan2_metadata" /> + </param> + + <param name="bowtie2db" label="BowTie2 database for MetaPhlAn2" type="select" > + <options from_data_table="metaphlan2_bowtie_db" /> + </param> + <param name="nucleotide_database" label="Nucleotide database" type="select" > <options from_data_table="humann2_nucleotide_database" /> </param>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/metaphlan2_bowtie_db.loc.sample Tue Apr 12 03:06:03 2016 -0400 @@ -0,0 +1,5 @@ +# Bowtie2 db have to be downloaded from https://bitbucket.org/biobakery/metaphlan2/src/5424bb911dfc/db_v20/?at=default (whole directory) +# +#Since MetaPhlAn comes bundled with 1 Bowtie2 database, you can use it +#by downloading it as explained above and uncommenting the following lines. +#bowtie_db_v20 Defaut BowTie2 database $METAPHLAN2_DIR/db_v20/mpa_v20_m200
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/metaphlan2_metadata.loc.sample Tue Apr 12 03:06:03 2016 -0400 @@ -0,0 +1,5 @@ +#Metadata have to be downloaded from https://bitbucket.org/biobakery/metaphlan2/raw/5424bb911dfcdb7212ea0949d4faeb6e69cfa61f/db_v20/mpa_v20_m200.pkl +# +#Since MetaPhlAn comes bundled with 1 metadata database, you can use it +#by downloading it as explained above and uncommenting the following lines. +#metadata_db_v20 Defaut MetaPhlAn2 metadata $METAPHLAN2_DIR/db_v20/mpa_v20_m200.pkl
--- a/tool_data_table_conf.xml.sample Thu Mar 31 03:35:17 2016 -0400 +++ b/tool_data_table_conf.xml.sample Tue Apr 12 03:06:03 2016 -0400 @@ -8,4 +8,12 @@ <columns>value, name, path</columns> <file path="tool-data/humann2_nucleotide_database.loc" /> </table> + <table name="metaphlan2_metadata" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/metaphlan2_metadata.loc" /> + </table> + <table name="metaphlan2_bowtie_db" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/metaphlan2_bowtie_db.loc" /> + </table> </tables>
--- a/tool_dependencies.xml Thu Mar 31 03:35:17 2016 -0400 +++ b/tool_dependencies.xml Tue Apr 12 03:06:03 2016 -0400 @@ -4,7 +4,7 @@ <repository changeset_revision="f5582ac5ba3c" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="metaphlan2" version="2.2.0"> - <repository changeset_revision="bbac0ef27bb2" name="package_metaphlan2_2_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="3cb6227f905e" name="package_metaphlan2_2_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="diamond" version="0.7.10"> <repository changeset_revision="f3f009bdca19" name="package_diamond_0_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />