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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="exclude_seqs_by_blast" name="exclude_seqs_by_blast" version="1.2.0">
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2 <description>Exclude contaminated sequences using BLAST</description>
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3 <requirements>
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4 <requirement type="binary">exclude_seqs_by_blast.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='$__new_file_path__'
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9 exclude_seqs_by_blast.py
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10 --querydb=$querydb
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11 --subjectdb=$subjectdb
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12 --outputfilename=$outputfilename
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13 --e_value=$e_value
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14 --percent_aligned=$percent_aligned
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15 $no_clean
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16 --blastmatroot=$blastmatroot
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17 --working_dir=$working_dir
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18 --max_hits=$max_hits
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19 --word_size=$word_size
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20 $no_format_db
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21 </command>
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22 <inputs>
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23 <param name="querydb" type="text" label="querydb"
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24 help="The path to a FASTA file containing query sequences [REQUIRED]"/>
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25 <param name="subjectdb" type="text" label="subjectdb"
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26 help="The path to a FASTA file to BLAST against [REQUIRED]"/>
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27 <param name="e_value" type="float" value="1e-10" label="e_value"
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28 help="The e-value cutoff for blast queries [default: 1e-10]."/>
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29 <param name="percent_aligned" type="float" value="0.97" label="percent_aligned"
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30 help="The % alignment cutoff for blast queries [default: 0.97]."/>
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31 <param name="no_clean" type="boolean" truevalue="--no_clean" falsevalue="" checked="false" label="no_clean"
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32 help="If set, don't delete files generated by formatdb after running [default: False]."/>
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33 <param name="blastmatroot" type="text" label="blastmatroot"
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34 help="Path to a folder containing blast matrices [default: %default]."/>
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35 <param name="working_dir" type="text" value="/tmp" label="working_dir"
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36 help="Working dir for BLAST [default: /tmp]."/>
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37 <param name="max_hits" type="integer" value="100" label="max_hits"
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38 help="Max hits parameter for BLAST. CAUTION: Because filtering on alignment percentage occurs after BLAST, a max hits value of 1 in combination with an alignment percent filter could miss valid contaminants. [default: 100]"/>
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39 <param name="word_size" type="integer" value="28" label="word_size"
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40 help="Word size to use for BLAST search [default: 28]"/>
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41 <param name="no_format_db" type="boolean" truevalue="--no_format_db" falsevalue="" checked="false" label="no_format_db"
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42 help="If this flag is specified, format_db will not be called on the subject database (formatdb will be set to False). This is useful if you have already formatted the database and a) it took a very long time or b) you want to run the script in parallel on the pre-formatted database [default: False]"/>
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43 </inputs>
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44 <outputs>
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45 <data format="txt" name="outputfilename"/>
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46 </outputs>
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47 <tests>
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48 </tests>
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49 <help>
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50
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51 </help>
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52 </tool>
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