Mercurial > repos > ulfschaefer > phemost
comparison MOST.xml @ 0:653407a0018e draft default tip
Uploaded
| author | ulfschaefer |
|---|---|
| date | Wed, 13 Jul 2016 06:12:58 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:653407a0018e |
|---|---|
| 1 <tool id="most" name="MOST"> | |
| 2 <description>Determine MLST from sequencing reads</description> | |
| 3 | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2.7.10">python</requirement> | |
| 6 <requirement type="package" version="3.2.3">lxml</requirement> | |
| 7 <requirement type="package" version="3.11">pyyaml</requirement> | |
| 8 <requirement type="package" version="1.9">numpy</requirement> | |
| 9 <requirement type="package" version="1.66">biopython</requirement> | |
| 10 <requirement type="package" version="2.1.0">bowtie2</requirement> | |
| 11 <requirement type="package" version="0.1.18">samtools</requirement> | |
| 12 <requirement type="package" version="5.0.0">emboss</requirement> | |
| 13 <requirement type="package" version="2.2.27">blast+</requirement> | |
| 14 <requirement type="package" version="1.0">phemost</requirement> | |
| 15 </requirements> | |
| 16 | |
| 17 <command interpreter="bash"> | |
| 18 MOST.sh | |
| 19 $fwd_file | |
| 20 $rev_file | |
| 21 $out1 | |
| 22 $out2 | |
| 23 "${organism.fields.file_path}" | |
| 24 </command> | |
| 25 | |
| 26 <inputs> | |
| 27 <param name="fwd_file" type="data" format="fastq" label="Read dataset for direction 1" help="Select fastq R1 here."/> | |
| 28 <param name="rev_file" type="data" format="fastq" label="Read dataset for direction 2" help="Select fastq R2 here."/> | |
| 29 <param name="organism" type="select" label="Select an organism"> | |
| 30 <options from_data_table="mlst_data"> | |
| 31 <column name="value" index="0"/> | |
| 32 <column name="dbkey" index="1"/> | |
| 33 <column name="name" index="2"/> | |
| 34 <column name="time_stamp" index="3"/> | |
| 35 <column name="file_path" index="4"/> | |
| 36 <validator type="no_options" message="No indexes are available" /> | |
| 37 </options> | |
| 38 </param> | |
| 39 </inputs> | |
| 40 | |
| 41 <outputs> | |
| 42 <data name="out1" format="xml" label="${fwd_file.name}: MLST result XML"/> | |
| 43 <data name="out2" format="csv" label="${fwd_file.name}: MLST result CSV"/> | |
| 44 </outputs> | |
| 45 | |
| 46 <help> | |
| 47 https://github.com/phe-bioinformatics/MOST | |
| 48 </help> | |
| 49 </tool> |