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1 <tool id="ribopicker" name="riboPicker" version="1.0.0">
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2 <description>Easy identification and removal of rRNA-like sequences.</description>
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3 <version_command>ribopicker.pl -version | awk '{print $3}'</version_command>
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4 <command interpreter="bash">ribopicker.sh
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5 -id 'galaxy'
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6 #if $identity_threshold:
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7 -i $identity_threshold
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8 #end if
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9 #if $coverage_threshold:
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10 -c $coverage_threshold
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11 #end if
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12 #if $length_threshold:
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13 -l $length_threshold
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14 #end if
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15 #if $read_chunk_size:
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16 -S $read_chunk_size
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17 #end if
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18 #if $z_best_value:
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19 -z $z_best_value
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20 #end if
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21 #if $align_score_threshold:
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22 -T $align_score_threshold
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23 #end if
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24 -f $input
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25 </command>
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26 <inputs>
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27 <param name="input" type="data" format="fastq,fasta" label="from"
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28 help="Input file in FASTA or FASTQ format that contains the query
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29 sequences."/>
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30 <param name="dbs" type="select" label="Reference Database">
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31 <options from_data_table="ribopicker_dbs">
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32 <filter type="sort_by" column="2" />
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33 <validator type="no_options" message="No reference databases are available" />
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34 </options>
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35 </param>
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36 <param name="identity_threshold" type="integer" value="" size="3"
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37 label="Alignment Identity Threshold" optional="True" help="Alignment
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38 identity threshold in percentage (integer from 1-100 without %) used to
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39 define matching sequences as similar. The identity is calculated for the
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40 part of the query sequence that is aligned to a reference sequence. For
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41 example, a query sequence of 100 bp that aligns to a reference sequence
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42 over the first 50 bp with 40 matching positions has an identity value of
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43 80%." >
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44 <validator type="in_range" message="(1-100)" min="1" max="100"/>
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45 </param>
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46 <param name="coverage_threshold" type="integer" value="" size="3"
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47 label="Alignment Coverage Threshold" optional="True" help="Alignment
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48 coverage threshold in percentage (integer from 1-100 without %) used to
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49 define matching sequences as similar. The coverage is calculated for the
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50 part of the query sequence that is aligned to a reference sequence. For
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51 example, a query sequence of 100 bp that aligns to a reference sequence
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52 over the first 50 bp with 40 matching positions has an coverage value of
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53 50%." >
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54 <validator type="in_range" message="(1-100)" min="1" max="100"/>
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55 </param>
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56 <param name="length_threshold" type="integer" value="" size="5"
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57 label="Alignment Length Threshold" optional="True" help="Alignment
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58 length threshold used to define matching sequences as similar. For
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59 example, a query sequence of 100 bp that aligns to a reference sequence
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60 over the first 50 bp with 40 matching positions has an alignment length
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61 of 50." >
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62 <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
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63 </param>
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64 <param name="read_chunk_size" type="integer" value="" size="9"
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65 label="Chunk size of reads in bp for BWA-SW" optional="True" help="Chunk
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66 size of reads in bp as used by BWA-SW (default: 10000000)" >
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67 <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
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68 </param>
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69 <param name="z_best_value" type="integer" value="" size="5"
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70 label="Z-best value for BWA-SW" optional="True" help="Z-best value as
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71 used by BWA-SW (default: 1)">
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72 <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
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73 </param>
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74 <param name="align_score_threshold" type="integer" value="" size="5"
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75 label="Alignment score threshold for BWA-SW" optional="True"
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76 help="Alignment score threshold as used by BWA-SW (default: 30)" >
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77 <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
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78 </param>
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79 </inputs>
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80 <outputs>
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81 <data name="rrna" format="fasta" from_work_dir="galaxy_rrna.txt" label="rRNA" />
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82 <data name="nonrrna" format="fasta" from_work_dir="galaxy_nonrrna.txt" label="Non-rRNA" />
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83 </outputs>
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84 <!--
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85 Usage:
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86 ribopicker [options] -f <file> -dbs <list> ...
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87 Options:
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88 -T <integer>
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89 Alignment score threshold as used by BWA-SW (default: 30).
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90 -->
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91 <help>
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92 **What it does**
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93
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94 The riboPicker tool can be used to automatically identify and efficiently
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95 remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.
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96 </help>
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97 </tool>
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