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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="adjust_seq_orientation" name="adjust_seq_orientation" version="1.2.0">
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2 <description>Get the reverse complement of all sequences</description>
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3 <requirements>
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4 <requirement type="binary">adjust_seq_orientation.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='$__new_file_path__'
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9 adjust_seq_orientation.py
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10 --input_fasta_fp=$input_fasta_fp
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11 --output_fp=$output_fp
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12 $retain_seq_id
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13 </command>
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14 <inputs>
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15 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
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16 help="path to the input fasta file [REQUIRED]"/>
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17 <param name="retain_seq_id" type="boolean" truevalue="--retain_seq_id" falsevalue="" checked="false" label="retain_seq_id"
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18 help="leave seq description lines untouched [default: append ' RC' to seq description lines]"/>
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19 </inputs>
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20 <outputs>
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21 <data format="txt" name="output_fp" label="${tool.name} on ${on_string}: (RC)"/>
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22 </outputs>
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23 <tests>
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24 </tests>
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25 <help>
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26
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27 </help>
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28 </tool>
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