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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="filter_fasta" name="filter_fasta" version="1.2.0">
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2 <description>This script can be applied to remove sequences from a fasta file based on input criteria.</description>
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3 <requirements>
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4 <requirement type="binary">filter_fasta.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='$__new_file_path__'
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9 filter_fasta.py
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10 --input_fasta_fp=$input_fasta_fp
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11 --output_fasta_fp=$output_fasta_fp
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12 --otu_map=$otu_map
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13 --seq_id_fp=$seq_id_fp
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14 --subject_fasta_fp=$subject_fasta_fp
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15 --seq_id_prefix=$seq_id_prefix
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16 $negate
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17 </command>
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18 <inputs>
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19 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
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20 help="path to the input fasta file [REQUIRED]"/>
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21 <param name="otu_map" type="data" format="tabular" label="otu_map"
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22 help="an OTU map where sequences ids are those which should be retained"/>
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23 <param name="seq_id_fp" type="data" format="txt" label="seq_id_fp"
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24 help="A list of sequence identifiers (or tab-delimited lines with a seq identifier in the first field) which should be retained"/>
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25 <param name="subject_fasta_fp" type="data" format="fasta" label="subject_fasta_fp"
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26 help="A fasta file where the seq ids should be retained."/>
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27 <param name="seq_id_prefix" type="text" label="seq_id_prefix"
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28 help="keep seqs where seq_id starts with this prefix"/>
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29 <param name="negate" type="boolean" truevalue="--negate" falsevalue="" checked="false" label="negate"
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30 help="discard passed seq ids rather than keep passed seq ids [default: False]"/>
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31 </inputs>
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32 <outputs>
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33 <data format="txt" name="output_fasta_fp"/>
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34 </outputs>
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35 <tests>
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36 </tests>
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37 <help>
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38
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39 </help>
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40 </tool>
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