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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="split_libraries_illumina" name="split_libraries_illumina" version="1.2.0">
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2 <description>Script for processing raw Illumina Genome Analyzer II data.</description>
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3 <requirements>
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4 <requirement type="binary">split_libraries_illumina.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='$__new_file_path__'
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9 split_libraries_illumina.py
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10 --mapping_fp=$mapping_fp
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11 --five_prime_read_fp=$five_prime_read_fp
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12 --three_prime_read_fp=$three_prime_read_fp
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13 --output_dir=$__new_file_path__
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14 $store_unassigned
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15 --quality_threshold=$quality_threshold
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16 --max_bad_run_length=$max_bad_run_length
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17 --min_per_read_length=$min_per_read_length
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18 --sequence_max_n=$sequence_max_n
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19 --start_seq_id=$start_seq_id
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20 $rev_comp_barcode
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21 $barcode_in_header
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22 </command>
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23 <inputs>
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24 <param name="mapping_fp" type="data" format="tabular" label="mapping_fp"
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25 help="the mapping filepath [REQUIRED]"/>
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26 <param name="five_prime_read_fp" type="data" format="txt" label="five_prime_read_fp"
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27 help="the 5' read filepath [default: ('NO', 'DEFAULT')]"/>
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28 <param name="three_prime_read_fp" type="data" format="txt" label="three_prime_read_fp"
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29 help="the 3' read filepath [default: ('NO', 'DEFAULT')]"/>
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30 <param name="store_unassigned" type="boolean" truevalue="--store_unassigned" falsevalue="" checked="false" label="store_unassigned"
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31 help="store seqs which can't be assigned to samples because of unknown barcodes [default: False]"/>
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32 <param name="quality_threshold" type="float" value="1e-05" label="quality_threshold"
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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]"/>
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34 <param name="max_bad_run_length" type="integer" value="1" label="max_bad_run_length"
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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]"/>
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36 <param name="min_per_read_length" type="integer" value="75" label="min_per_read_length"
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37 help="min number of consecutive high quality base calls to includea read (per single end read) [default: 75]"/>
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38 <param name="sequence_max_n" type="integer" value="0" label="sequence_max_n"
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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]"/>
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40 <param name="start_seq_id" type="integer" value="0" label="start_seq_id"
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41 help="start seq_ids as ascending integers beginning with start_seq_id[default: 0]"/>
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42 <param name="rev_comp_barcode" type="boolean" truevalue="--rev_comp_barcode" falsevalue="" checked="false" label="rev_comp_barcode"
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43 help="reverse compliment barcodes before lookup[default: False]"/>
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44 <param name="barcode_in_header" type="boolean" truevalue="--barcode_in_header" falsevalue="" checked="false" label="barcode_in_header"
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45 help="barcode is in header line (rather than beginning of sequence)[default: False]"/>
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46 </inputs>
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47 <outputs>
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48
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49 </outputs>
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50 <tests>
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51 </tests>
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52 <help>
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53
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54 </help>
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55 </tool>
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