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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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1 <tool id="filter_alignment" name="filter_alignment" version="1.2.0">
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2 <description>Filter sequence alignment by removing highly variable regions</description>
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3 <requirements>
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4 <requirement type="binary">filter_alignment.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='$__new_file_path__'
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9 --galaxy_outputdir='$pfiltered_fasta.extra_files_path'
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10 --galaxy_datasets='^\S+_pfiltered\.\S+$:'$pfiltered_fasta
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11 filter_alignment.py
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12 --input_fasta_file=$input_fasta_file
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13 --output_dir='$pfiltered_fasta.extra_files_path'
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14 --lane_mask_fp=$lane_mask_fp
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15 $suppress_lane_mask_filter
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16 --allowed_gap_frac=$allowed_gap_frac
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17 $remove_outliers
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18 --threshold=$threshold
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19 </command>
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20 <inputs>
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21 <param name="input_fasta_file" type="data" format="align" label="input_fasta_file"
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22 help="the input directory [REQUIRED]"/>
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23 <param name="lane_mask_fp" type="data" format="filter" label="lane_mask_fp"
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24 help="path to lanemask file [default: %default]"/>
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25 <param name="suppress_lane_mask_filter" type="boolean" truevalue="--suppress_lane_mask_filter" falsevalue="" checked="false" label="suppress_lane_mask_filter"
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26 help="suppress lane mask filtering (necessary to turn off lane-mask-based filtering when a qiime_config default is provided for --lane_mask_fp) [default: False]"/>
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27 <param name="allowed_gap_frac" type="float" value="0.999999" label="allowed_gap_frac"
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28 help="gap filter threshold, filters positions which are gaps in } allowed_gap_frac of the sequences [default: 0.999999]"/>
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29 <param name="remove_outliers" type="boolean" truevalue="--remove_outliers" falsevalue="" checked="false" label="remove_outliers"
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30 help="remove seqs very dissimilar to the alignment consensus (see --threshold). [default: False]"/>
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31 <param name="threshold" type="float" value="3.0" label="threshold"
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32 help="with -r, remove seqs whose dissimilarity to the consensus sequence is approximately } x standard devaitions above the mean of the sequences [default: 3.0]"/>
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33 </inputs>
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34 <outputs>
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35 <data format="align" name="pfiltered_fasta" label="${tool.name} on ${on_string}: pfiltered.fasta"/>
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36 </outputs>
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37 <tests>
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38 </tests>
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39 <help>
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40
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41 </help>
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42 </tool>
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