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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="extract_seqs_by_sample_id" name="extract_seqs_by_sample_id" version="1.2.0">
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2 <description>Extract sequences based on the SampleID</description>
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3 <requirements>
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4 <requirement type="binary">extract_seqs_by_sample_id.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='$__new_file_path__'
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9 extract_seqs_by_sample_id.py
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10 --input_fasta_fp=$input_fasta_fp
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11 --sample_ids=$sample_ids
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12 --output_fasta_fp=$output_fasta_fp
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13 $negate
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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="sample_ids" type="text" label="sample_ids"
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19 help="comma-separated sample_ids to include in output fasta file(or exclude if -n=True) [REQUIRED]"/>
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20 <param name="negate" type="boolean" truevalue="--negate" falsevalue="" checked="false" label="negate"
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21 help="negate the sample ID list (i.e., output sample ids not passed via -s) [default: False]"/>
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22 </inputs>
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23 <outputs>
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24 <data format="txt" name="output_fasta_fp"/>
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25 </outputs>
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26 <tests>
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27 </tests>
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28 <help>
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29
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30 </help>
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31 </tool>
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