Mercurial > repos > jjohnson > metaphlan
diff metaphlan.xml @ 5:61f300dbc6ac draft
Enable fastq input
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 10 Oct 2012 12:35:51 -0500 |
| parents | 3468e70d3ed0 |
| children | a3068eb6b676 |
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--- a/metaphlan.xml Wed Oct 10 08:49:28 2012 -0500 +++ b/metaphlan.xml Wed Oct 10 12:35:51 2012 -0500 @@ -4,8 +4,8 @@ <requirement type="package">bowtie2</requirement> </requirements> <description>Metagenomic Phylogenetic Analysis</description> - <command> - metaphlan.py + <command interpreter="python"> + \${METAPHLAN_PATH}/metaphlan.py $input --bowtie2db \${METAPHLAN_PATH}/bowtie2db/mpa --no_map @@ -14,9 +14,10 @@ </command> <inputs> - <param format="fasta" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param> + <param format="fasta,fastq" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param> <param name="PresetsForBowtie2" type="select" format="text"> <label>Sensitivity options for read-marker similarity (as described by BowTie2)</label> + <help>sensitive-local is recommended for avoiding overly-sensitive hits when using non-preprocessed fastq files</help> <option value="very-sensitive-local">Very Sensitive Local</option> <option value="sensitive-local">Sensitive Local</option> <option value="very-sensitive">Very Sensitive</option>