Mercurial > repos > jjohnson > qiime
view filter_alignment.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
author | Jim Johnson <jj@umn.edu> |
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date | Sun, 17 Jul 2011 10:30:11 -0500 |
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<tool id="filter_alignment" name="filter_alignment" version="1.2.0"> <description>Filter sequence alignment by removing highly variable regions</description> <requirements> <requirement type="binary">filter_alignment.py</requirement> </requirements> <command interpreter="python"> qiime_wrapper.py ## --galaxy_tmpdir='$__new_file_path__' --galaxy_outputdir='$pfiltered_fasta.extra_files_path' --galaxy_datasets='^\S+_pfiltered\.\S+$:'$pfiltered_fasta filter_alignment.py --input_fasta_file=$input_fasta_file --output_dir='$pfiltered_fasta.extra_files_path' --lane_mask_fp=$lane_mask_fp $suppress_lane_mask_filter --allowed_gap_frac=$allowed_gap_frac $remove_outliers --threshold=$threshold </command> <inputs> <param name="input_fasta_file" type="data" format="align" label="input_fasta_file" help="the input directory [REQUIRED]"/> <param name="lane_mask_fp" type="data" format="filter" label="lane_mask_fp" help="path to lanemask file [default: %default]"/> <param name="suppress_lane_mask_filter" type="boolean" truevalue="--suppress_lane_mask_filter" falsevalue="" checked="false" label="suppress_lane_mask_filter" 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]"/> <param name="allowed_gap_frac" type="float" value="0.999999" label="allowed_gap_frac" help="gap filter threshold, filters positions which are gaps in } allowed_gap_frac of the sequences [default: 0.999999]"/> <param name="remove_outliers" type="boolean" truevalue="--remove_outliers" falsevalue="" checked="false" label="remove_outliers" help="remove seqs very dissimilar to the alignment consensus (see --threshold). [default: False]"/> <param name="threshold" type="float" value="3.0" label="threshold" 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]"/> </inputs> <outputs> <data format="align" name="pfiltered_fasta" label="${tool.name} on ${on_string}: pfiltered.fasta"/> </outputs> <tests> </tests> <help> </help> </tool>