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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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e5c3175506b7 Initial tool configs for qiime, most need work.
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1 <tool id="make_fastq" name="make_fastq" version="1.2.0">
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2 <description>Make fastq file for ERA submission from paired fasta and qual files</description>
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3 <requirements>
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4 <requirement type="binary">make_fastq.py</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 qiime_wrapper.py
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8 --galaxy_tmpdir='$__new_file_path__'
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9 make_fastq.py
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10 --input_fasta_fp=$input_fasta_fp
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11 --qual=$qual
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12 --result_fp=$result_fp
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13 $split
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14 </command>
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15 <inputs>
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16 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
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17 help="path to the input fasta file [REQUIRED]"/>
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18 <param name="qual" type="data" format="qual" label="qual"
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19 help="names of qual files, comma-delimited [REQUIRED]"/>
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20 <param name="result_fp" type="data" format="txt" label="result_fp"
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21 help="Path to store results [default: {input_sequences_filename}.fastq]"/>
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22 <param name="split" type="boolean" truevalue="--split" falsevalue="" checked="false" label="split"
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23 help="make separate file for each library [default:False]"/>
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24 </inputs>
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25 <outputs>
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26
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27 </outputs>
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28 <tests>
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29 </tests>
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30 <help>
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31
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32 </help>
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33 </tool>
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