Mercurial > repos > bebatut > metaphlan2
changeset 5:167876cbcdd5 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 259ec654231c792a102f99ab7bfd63cbabd4874a-dirty
| author | bebatut |
|---|---|
| date | Wed, 28 Oct 2015 12:34:12 -0400 |
| parents | 575f1f4420ee |
| children | 9603321a8519 |
| files | metaphlan2.xml |
| diffstat | 1 files changed, 26 insertions(+), 17 deletions(-) [+] |
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--- a/metaphlan2.xml Wed Oct 28 12:29:53 2015 -0400 +++ b/metaphlan2.xml Wed Oct 28 12:34:12 2015 -0400 @@ -35,10 +35,14 @@ #if $analysis_type.analysis_type_select == "rel_ab" --tax_lev $analysis_type.taxonomic_level - #else if $analysis_type.analysis_type_select == "marker_ab_table" - --nreads $analysis_type.nreads - #else if $analysis_type.analysis_type_select == "marker_pres_table" - --pres_th $analysis_type.pres_th + #else + #if $analysis_type.analysis_type_select == "marker_ab_table" + --nreads $analysis_type.nreads + #else + #if $analysis_type.analysis_type_select == "marker_pres_table" + --pres_th $analysis_type.pres_th + #end if + #end if #end if --min_cu_len $min_cu_len @@ -163,16 +167,21 @@ Several parameters can modulate the MetaPhlAn execution -- Mapping arguments - - Test to avoid saving the output of BowTie2 -- Post-mapping arguments - - Taxonomic level for the relative abundance output - - Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances - - Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded - - Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea - - Quantile value -- Additional analysis types and arguments - - Type of analyse to perform and some parameters for specific analysis type +* Mapping arguments + + * Test to avoid saving the output of BowTie2 + +* Post-mapping arguments + + * Taxonomic level for the relative abundance output + * Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances + * Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded + * Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea + * Quantile value + +* Additional analysis types and arguments + + * Type of analyse to perform and some parameters for specific analysis type ----- @@ -183,9 +192,9 @@ Given the choosen parameters, other output files can be: -- a sam output file -- a biom output fime -- a BowTie2 output file +* a sam output file +* a biom output fime +* a BowTie2 output file ]]></help>