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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="blast_wrapper" name="blast_wrapper" version="1.2.0">
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2 <description>Blast Interface</description>
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3 <requirements>
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4 <requirement type="binary">blast_wrapper.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='$__new_file_path__'
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9 blast_wrapper.py
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10 --input_fasta_fp=$input_fasta_fp
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11 --refseqs_fp=$refseqs_fp
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12 --num_seqs_per_blast_run=$num_seqs_per_blast_run
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13 </command>
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14 <inputs>
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15 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
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16 help="path to the input fasta file [REQUIRED]"/>
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17 <param name="refseqs_fp" type="data" format="fasta" label="refseqs_fp"
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18 help="path to blast database as a fasta file [REQUIRED]"/>
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19 <param name="num_seqs_per_blast_run" type="integer" value="1000" label="num_seqs_per_blast_run"
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20 help="number of sequences passed to each blast call - useful for very large sequence collections [default: 1000]"/>
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21 </inputs>
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22 <outputs>
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23
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24 </outputs>
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25 <tests>
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26 </tests>
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27 <help>
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28
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29 </help>
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30 </tool>
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