Mercurial > repos > jjohnson > qiime
comparison filter_fasta.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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| -1:000000000000 | 0:e5c3175506b7 |
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| 1 <tool id="filter_fasta" name="filter_fasta" version="1.2.0"> | |
| 2 <description>This script can be applied to remove sequences from a fasta file based on input criteria.</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">filter_fasta.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_tmpdir='$__new_file_path__' | |
| 9 filter_fasta.py | |
| 10 --input_fasta_fp=$input_fasta_fp | |
| 11 --output_fasta_fp=$output_fasta_fp | |
| 12 --otu_map=$otu_map | |
| 13 --seq_id_fp=$seq_id_fp | |
| 14 --subject_fasta_fp=$subject_fasta_fp | |
| 15 --seq_id_prefix=$seq_id_prefix | |
| 16 $negate | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp" | |
| 20 help="path to the input fasta file [REQUIRED]"/> | |
| 21 <param name="otu_map" type="data" format="tabular" label="otu_map" | |
| 22 help="an OTU map where sequences ids are those which should be retained"/> | |
| 23 <param name="seq_id_fp" type="data" format="txt" label="seq_id_fp" | |
| 24 help="A list of sequence identifiers (or tab-delimited lines with a seq identifier in the first field) which should be retained"/> | |
| 25 <param name="subject_fasta_fp" type="data" format="fasta" label="subject_fasta_fp" | |
| 26 help="A fasta file where the seq ids should be retained."/> | |
| 27 <param name="seq_id_prefix" type="text" label="seq_id_prefix" | |
| 28 help="keep seqs where seq_id starts with this prefix"/> | |
| 29 <param name="negate" type="boolean" truevalue="--negate" falsevalue="" checked="false" label="negate" | |
| 30 help="discard passed seq ids rather than keep passed seq ids [default: False]"/> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="txt" name="output_fasta_fp"/> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 </tests> | |
| 37 <help> | |
| 38 | |
| 39 </help> | |
| 40 </tool> | |
| 41 |