Mercurial > repos > bebatut > metaphlan2
changeset 6:9603321a8519 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 259ec654231c792a102f99ab7bfd63cbabd4874a-dirty
| author | bebatut |
|---|---|
| date | Wed, 28 Oct 2015 12:37:13 -0400 |
| parents | 167876cbcdd5 |
| children | 4e4002bfc9b3 |
| files | metaphlan2.xml |
| diffstat | 1 files changed, 23 insertions(+), 26 deletions(-) [+] |
line wrap: on
line diff
--- a/metaphlan2.xml Wed Oct 28 12:34:12 2015 -0400 +++ b/metaphlan2.xml Wed Oct 28 12:37:13 2015 -0400 @@ -17,7 +17,8 @@ ]]> </version_command> - <command><![CDATA[ + <command> +<![CDATA[ python \${METAPHLAN2_DIR}/metaphlan.py $input_file -o $output_file @@ -35,14 +36,10 @@ #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 - #end if - #end if + #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 --min_cu_len $min_cu_len @@ -57,13 +54,13 @@ #if $sam_output -s $sam_output_file - #endif + #end if #if $biom_output -biom $biom_output_file - #endif - - ]]></command> + #end if +]]> + </command> <inputs> <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/> @@ -167,21 +164,21 @@ Several parameters can modulate the MetaPhlAn execution -* Mapping arguments + * Mapping arguments - * Test to avoid saving the output of BowTie2 + * Test to avoid saving the output of BowTie2 -* Post-mapping arguments + * 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 + * 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 + * Additional analysis types and arguments - * Type of analyse to perform and some parameters for specific analysis type + * Type of analyse to perform and some parameters for specific analysis type ----- @@ -192,9 +189,9 @@ 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>