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annotate transcriptsToOrfs.xml @ 5:a67c0a0d24ac

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Update samtools tool_dependency
author Jim Johnson <jj@umn.edu>
date Mon, 11 Nov 2013 11:15:53 -0600
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1 <tool id="transcriptsToOrfs" name="transcriptsToOrfs" version="0.0.2">
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2 <description>Trinity Transcripts to Candidate Peptides</description>
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3 <requirements>
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4 <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
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5 <requirement type="package" version="3.0">hmmer</requirement>
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6 </requirements>
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7 <command>
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8 \$TRINITY_HOME/trinity-plugins/transdecoder/transcripts_to_best_scoring_ORFs.pl
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9 -t $transcripts
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10 #if $min_prot_length:
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11 -m $min_prot_length
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12 #end if
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13 #if $retain_long_orfs:
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14 --retain_long_orfs $retain_long_orfs
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15 #end if
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16 #if $training_count:
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17 -T $training_count
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18 #end if
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19 #if str($strand_specificity) == 'SS':
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20 -S
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21 #end if
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22 #if $genetic_code.__str__ != '':
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23 -G $genetic_code
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24 #end if
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25 #if $search.use_pfam == 'yes':
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26 --search_pfam "${ filter( lambda x: str( x[0] ) == str( $search.pfam_db ), $__app__.tool_data_tables[ 'pfam_databases' ].get_fields() )[0][-1] }"
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27 --CPU $search.CPU
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28 #end if
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29 </command>
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30 <inputs>
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31 <param format="fasta" name="transcripts" type="data" label="Transcripts sequences in fastA format" help="" />
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32 <param name="min_prot_length" type="integer" value="" optional="true" label="Minimum peptide length (in amino acids)" help="default: 100">
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33 <validator type="in_range" message="Minimum peptide length should be at least 50" min="50" />
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34 </param>
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35 <param name="retain_long_orfs" type="integer" value="" optional="true" label="Retain all ORFs found that are of minimum length in nucleotides" help="default: 900" >
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36 <validator type="in_range" message="ORF length should be at least 50" min="50" />
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37 </param>
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38 <param name="training_count" type="integer" value="" optional="true" label="Number of top longest ORFs to train Markov Model (hexamer stats)" help="default: 500" >
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39 <validator type="in_range" message="ORF count should be at least 50" min="50" />
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40 </param>
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41 <param name="strand_specificity" type="select" label="Strand specificity type">
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42 <option value="DS">NOT strand specific, examine both strands</option>
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43 <option value="SS">Strand specific, examine only top strand</option>
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44 </param>
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45 <param name="genetic_code" type="select" label="Genetic Code">
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46 <option value="">use default(universal)</option>
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47 <option value="universal">universal</option>
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48 <option value="Euplotes">Euplotes</option>
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49 <option value="Tetrahymena">Tetrahymena</option>
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50 <option value="Candida">Candida</option>
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51 <option value="Acetabularia">Acetabularia</option>
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52 </param>
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53 <conditional name="search">
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54 <param name="use_pfam" type="select" label="Search PFAM database">
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55 <option value="no">NO</option>
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56 <option value="yes">YES</option>
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57 </param>
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58 <when value="no"/>
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59 <when value="yes">
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60 <param name="pfam_db" type="select" label="Pfam database">
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61 <options from_data_table="pfam_databases" />
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62 </param>
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63 <param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by hmmscan" />
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64 </when>
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65 </conditional>
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66 </inputs>
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67 <stdio>
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68 <exit_code range="1:" level="fatal" description="Failed" />
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69 <regex match="Error"
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70 source="stderr"
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71 level="fatal"
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72 description="Failed" />
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73 </stdio>
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74 <outputs>
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75 <data format="txt" name="trinity_pep_pfam" label="${tool.name} on ${on_string}: Pfam matches to Candidate Peptide Sequences" from_work_dir="longest_orfs.pep.pfam.dat">
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76 <filter>search['use_pfam'] == 'yes'</filter>
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77 </data>
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78 <data format="gff3" name="trinity_pep_gff3" label="${tool.name} on ${on_string} Candidate Peptide Features" from_work_dir="best_candidates.eclipsed_orfs_removed.gff3" />
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79 <data format="bed" name="trinity_pep_bed" label="${tool.name} on ${on_string} Candidate Peptide Coordinates" from_work_dir="best_candidates.eclipsed_orfs_removed.bed" />
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80 <data format="fasta" name="trinity_pep_cds" label="${tool.name} on ${on_string}: Candidate Peptide CDS Sequences" from_work_dir="best_candidates.eclipsed_orfs_removed.cds"/>
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81 <data format="fasta" name="trinity_pep_seqs" label="${tool.name} on ${on_string}: Candidate Peptide Sequences" from_work_dir="best_candidates.eclipsed_orfs_removed.pep"/>
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="transcripts" ftype="fasta" value="TrinitySingle.fasta"/>
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86 <param name="min_prot_length" value="100"/>
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87 <param name="use_pfam" value="no"/>
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88 <output name="trinity_pep_seqs">
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89 <assert_contents>
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90 <has_text text="WAAKAWLITARSLYPADF" />
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91 </assert_contents>
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92 </output>
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93 <output name="trinity_pep_cds">
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94 <assert_contents>
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95 <has_text text="TGGGCAGCCAAGGCATGGCTGATCACGGCCCGCA" />
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96 </assert_contents>
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97 </output>
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98 <output name="trinity_pep_bed">
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99 <assert_contents>
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100 <has_text text="comp10_c0_seq1" />
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101 </assert_contents>
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102 </output>
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103 <output name="trinity_pep_gff3">
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104 <assert_contents>
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105 <has_text text="comp10_c0_seq1" />
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106 </assert_contents>
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107 </output>
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108 </test>
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109 </tests>
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110 <help>
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111 ** transcriptsToOrfs **
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112 Trinity_ is a de novo transcript assembler that uses RNA-seq data as input.
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113 This tool searches for open reading frames in the assembled transcripts.
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114
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115 .. _Trinity: http://trinityrnaseq.sourceforge.net
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116 </help>
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117 </tool>