Mercurial > repos > malex > ribopicker
comparison ribopicker.xml @ 0:75ca0166e969 draft
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| author | malex |
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| date | Tue, 16 Oct 2012 19:42:32 -0400 |
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| -1:000000000000 | 0:75ca0166e969 |
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| 1 <tool id="ribopicker" name="riboPicker" version="1.0.0"> | |
| 2 <description>Easy identification and removal of rRNA-like sequences.</description> | |
| 3 <version_command>ribopicker.pl -version | awk '{print $3}'</version_command> | |
| 4 <command interpreter="bash">ribopicker.sh | |
| 5 -id 'galaxy' | |
| 6 #if $identity_threshold: | |
| 7 -i $identity_threshold | |
| 8 #end if | |
| 9 #if $coverage_threshold: | |
| 10 -c $coverage_threshold | |
| 11 #end if | |
| 12 #if $length_threshold: | |
| 13 -l $length_threshold | |
| 14 #end if | |
| 15 #if $read_chunk_size: | |
| 16 -S $read_chunk_size | |
| 17 #end if | |
| 18 #if $z_best_value: | |
| 19 -z $z_best_value | |
| 20 #end if | |
| 21 #if $align_score_threshold: | |
| 22 -T $align_score_threshold | |
| 23 #end if | |
| 24 -f $input | |
| 25 </command> | |
| 26 <inputs> | |
| 27 <param name="input" type="data" format="fastq,fasta" label="from" | |
| 28 help="Input file in FASTA or FASTQ format that contains the query | |
| 29 sequences."/> | |
| 30 <param name="dbs" type="select" label="Reference Database"> | |
| 31 <options from_data_table="ribopicker_dbs"> | |
| 32 <filter type="sort_by" column="2" /> | |
| 33 <validator type="no_options" message="No reference databases are available" /> | |
| 34 </options> | |
| 35 </param> | |
| 36 <param name="identity_threshold" type="integer" value="" size="3" | |
| 37 label="Alignment Identity Threshold" optional="True" help="Alignment | |
| 38 identity threshold in percentage (integer from 1-100 without %) used to | |
| 39 define matching sequences as similar. The identity is calculated for the | |
| 40 part of the query sequence that is aligned to a reference sequence. For | |
| 41 example, a query sequence of 100 bp that aligns to a reference sequence | |
| 42 over the first 50 bp with 40 matching positions has an identity value of | |
| 43 80%." > | |
| 44 <validator type="in_range" message="(1-100)" min="1" max="100"/> | |
| 45 </param> | |
| 46 <param name="coverage_threshold" type="integer" value="" size="3" | |
| 47 label="Alignment Coverage Threshold" optional="True" help="Alignment | |
| 48 coverage threshold in percentage (integer from 1-100 without %) used to | |
| 49 define matching sequences as similar. The coverage is calculated for the | |
| 50 part of the query sequence that is aligned to a reference sequence. For | |
| 51 example, a query sequence of 100 bp that aligns to a reference sequence | |
| 52 over the first 50 bp with 40 matching positions has an coverage value of | |
| 53 50%." > | |
| 54 <validator type="in_range" message="(1-100)" min="1" max="100"/> | |
| 55 </param> | |
| 56 <param name="length_threshold" type="integer" value="" size="5" | |
| 57 label="Alignment Length Threshold" optional="True" help="Alignment | |
| 58 length threshold used to define matching sequences as similar. For | |
| 59 example, a query sequence of 100 bp that aligns to a reference sequence | |
| 60 over the first 50 bp with 40 matching positions has an alignment length | |
| 61 of 50." > | |
| 62 <validator type="in_range" message="(1-infinity)" min="1" max="inf"/> | |
| 63 </param> | |
| 64 <param name="read_chunk_size" type="integer" value="" size="9" | |
| 65 label="Chunk size of reads in bp for BWA-SW" optional="True" help="Chunk | |
| 66 size of reads in bp as used by BWA-SW (default: 10000000)" > | |
| 67 <validator type="in_range" message="(1-infinity)" min="1" max="inf"/> | |
| 68 </param> | |
| 69 <param name="z_best_value" type="integer" value="" size="5" | |
| 70 label="Z-best value for BWA-SW" optional="True" help="Z-best value as | |
| 71 used by BWA-SW (default: 1)"> | |
| 72 <validator type="in_range" message="(1-infinity)" min="1" max="inf"/> | |
| 73 </param> | |
| 74 <param name="align_score_threshold" type="integer" value="" size="5" | |
| 75 label="Alignment score threshold for BWA-SW" optional="True" | |
| 76 help="Alignment score threshold as used by BWA-SW (default: 30)" > | |
| 77 <validator type="in_range" message="(1-infinity)" min="1" max="inf"/> | |
| 78 </param> | |
| 79 </inputs> | |
| 80 <outputs> | |
| 81 <data name="rrna" format="fasta" from_work_dir="galaxy_rrna.txt" label="rRNA" /> | |
| 82 <data name="nonrrna" format="fasta" from_work_dir="galaxy_nonrrna.txt" label="Non-rRNA" /> | |
| 83 </outputs> | |
| 84 <!-- | |
| 85 Usage: | |
| 86 ribopicker [options] -f <file> -dbs <list> ... | |
| 87 Options: | |
| 88 -T <integer> | |
| 89 Alignment score threshold as used by BWA-SW (default: 30). | |
| 90 --> | |
| 91 <help> | |
| 92 **What it does** | |
| 93 | |
| 94 The riboPicker tool can be used to automatically identify and efficiently | |
| 95 remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. | |
| 96 </help> | |
| 97 </tool> |