Mercurial > repos > jjohnson > qiime
comparison split_libraries_illumina.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="split_libraries_illumina" name="split_libraries_illumina" version="1.2.0"> | |
| 2 <description>Script for processing raw Illumina Genome Analyzer II data.</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">split_libraries_illumina.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_tmpdir='$__new_file_path__' | |
| 9 split_libraries_illumina.py | |
| 10 --mapping_fp=$mapping_fp | |
| 11 --five_prime_read_fp=$five_prime_read_fp | |
| 12 --three_prime_read_fp=$three_prime_read_fp | |
| 13 --output_dir=$__new_file_path__ | |
| 14 $store_unassigned | |
| 15 --quality_threshold=$quality_threshold | |
| 16 --max_bad_run_length=$max_bad_run_length | |
| 17 --min_per_read_length=$min_per_read_length | |
| 18 --sequence_max_n=$sequence_max_n | |
| 19 --start_seq_id=$start_seq_id | |
| 20 $rev_comp_barcode | |
| 21 $barcode_in_header | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param name="mapping_fp" type="data" format="tabular" label="mapping_fp" | |
| 25 help="the mapping filepath [REQUIRED]"/> | |
| 26 <param name="five_prime_read_fp" type="data" format="txt" label="five_prime_read_fp" | |
| 27 help="the 5' read filepath [default: ('NO', 'DEFAULT')]"/> | |
| 28 <param name="three_prime_read_fp" type="data" format="txt" label="three_prime_read_fp" | |
| 29 help="the 3' read filepath [default: ('NO', 'DEFAULT')]"/> | |
| 30 <param name="store_unassigned" type="boolean" truevalue="--store_unassigned" falsevalue="" checked="false" label="store_unassigned" | |
| 31 help="store seqs which can't be assigned to samples because of unknown barcodes [default: False]"/> | |
| 32 <param name="quality_threshold" type="float" value="1e-05" label="quality_threshold" | |
| 33 help="max base call error probability to consider high-quality (probability of base call being error, so values closer to 1 mean that the base call is more likely to be erroneous) [default: 1e-05]"/> | |
| 34 <param name="max_bad_run_length" type="integer" value="1" label="max_bad_run_length" | |
| 35 help="max number of consecutive low quality base calls allowed before truncating a read [default: 1; the read is trucated at thesecond low quality call]"/> | |
| 36 <param name="min_per_read_length" type="integer" value="75" label="min_per_read_length" | |
| 37 help="min number of consecutive high quality base calls to includea read (per single end read) [default: 75]"/> | |
| 38 <param name="sequence_max_n" type="integer" value="0" label="sequence_max_n" | |
| 39 help="maximum number of N characters allowed in a sequence to retain it -- this is applied after quality trimming, and is total over combined paired end reads if applicable [default: 0]"/> | |
| 40 <param name="start_seq_id" type="integer" value="0" label="start_seq_id" | |
| 41 help="start seq_ids as ascending integers beginning with start_seq_id[default: 0]"/> | |
| 42 <param name="rev_comp_barcode" type="boolean" truevalue="--rev_comp_barcode" falsevalue="" checked="false" label="rev_comp_barcode" | |
| 43 help="reverse compliment barcodes before lookup[default: False]"/> | |
| 44 <param name="barcode_in_header" type="boolean" truevalue="--barcode_in_header" falsevalue="" checked="false" label="barcode_in_header" | |
| 45 help="barcode is in header line (rather than beginning of sequence)[default: False]"/> | |
| 46 </inputs> | |
| 47 <outputs> | |
| 48 | |
| 49 </outputs> | |
| 50 <tests> | |
| 51 </tests> | |
| 52 <help> | |
| 53 | |
| 54 </help> | |
| 55 </tool> | |
| 56 |