Mercurial > repos > ulfschaefer > phemost
diff MOST.xml @ 0:653407a0018e draft default tip
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| author | ulfschaefer |
|---|---|
| date | Wed, 13 Jul 2016 06:12:58 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MOST.xml Wed Jul 13 06:12:58 2016 -0400 @@ -0,0 +1,49 @@ +<tool id="most" name="MOST"> + <description>Determine MLST from sequencing reads</description> + + <requirements> + <requirement type="package" version="2.7.10">python</requirement> + <requirement type="package" version="3.2.3">lxml</requirement> + <requirement type="package" version="3.11">pyyaml</requirement> + <requirement type="package" version="1.9">numpy</requirement> + <requirement type="package" version="1.66">biopython</requirement> + <requirement type="package" version="2.1.0">bowtie2</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + <requirement type="package" version="5.0.0">emboss</requirement> + <requirement type="package" version="2.2.27">blast+</requirement> + <requirement type="package" version="1.0">phemost</requirement> + </requirements> + + <command interpreter="bash"> + MOST.sh + $fwd_file + $rev_file + $out1 + $out2 + "${organism.fields.file_path}" + </command> + + <inputs> + <param name="fwd_file" type="data" format="fastq" label="Read dataset for direction 1" help="Select fastq R1 here."/> + <param name="rev_file" type="data" format="fastq" label="Read dataset for direction 2" help="Select fastq R2 here."/> + <param name="organism" type="select" label="Select an organism"> + <options from_data_table="mlst_data"> + <column name="value" index="0"/> + <column name="dbkey" index="1"/> + <column name="name" index="2"/> + <column name="time_stamp" index="3"/> + <column name="file_path" index="4"/> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + </inputs> + + <outputs> + <data name="out1" format="xml" label="${fwd_file.name}: MLST result XML"/> + <data name="out2" format="csv" label="${fwd_file.name}: MLST result CSV"/> + </outputs> + + <help> + https://github.com/phe-bioinformatics/MOST + </help> +</tool>