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annotate kobas_annotate.xml @ 3:83b998fa34ea draft

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author iuc
date Thu, 10 Nov 2016 16:21:41 -0500
parents 720b1beabad6
children 20f1b45dea63
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1 <tool id="kobas_annotate" name="KOBAS Annotate" version="@WRAPPER_VERSION@">
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2 <description>KEGG Orthology Based Annotation System</description>
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3 <macros>
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4 <import>kobas_macros.xml</import>
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5 </macros>
3
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6
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7 <expand macro="requirements"/>
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8
0
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9 <stdio>
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10 <exit_code range="0" level="warning" description="BiopythonDeprecationWarning"/>
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11 <exit_code range="1" level="fatal" description="Bad input settings or none of the entries was annotated successfully."/>
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12 </stdio>
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13 <command>
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14 <![CDATA[
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15
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16 ## create the KOBAS directories
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17 mkdir sqlite &&
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18 mkdir seq_pep &&
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19
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20 #if $blast_opts.choice == 'local':
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21 #set $blast_path = $blast_opts.localdb.fields.path
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22 #else if $blast_opts.choice == 'fasta':
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23 makeblastdb
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24 -in '$blast_opts.fastadb'
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25 -dbtype 'prot'
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26 -out 'seq_pep/${species}.pep.fasta' &&
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27 #else:
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28 #set $blast_path = $os.path.join($blast_opts.histdb.extra_files_path,'blastdb')
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29 #end if
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30
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31 ## create the database symlinks to comply with how KOBAS wants them
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32 ln -s '$organismdb' sqlite/organism.db &&
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33 ln -s '$kobasdb' 'sqlite/${species}.db' &&
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34
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35 #if $blast_opts.choice != 'fasta':
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36 ln -s '${blast_path}.phr' 'seq_pep/${species}.pep.fasta.phr' &&
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37 ln -s '${blast_path}.pin' 'seq_pep/${species}.pep.fasta.pin' &&
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38 ln -s '${blast_path}.psq' 'seq_pep/${species}.pep.fasta.psq' && ls -l seq_pep/ &&
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39 #end if
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40
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41 ## create the orthologe database symlinks to comply with how KOBAS wants them
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42 #if $ortholog.only == 'YES' and str($ortholog.species) != str($species):
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43
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44 #if $ortholog.blast_opts_ortholog.choice == 'local':
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45 #set $blast_path = $ortholog.blast_opts_ortholog.localdb.fields.path
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46 #else if $ortholog.blast_opts_ortholog.choice == 'fasta':
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47 makeblastdb
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48 -in '$ortholog.blast_opts_ortholog.fastadb'
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49 -dbtype 'prot'
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50 -out 'seq_pep/${ortholog.species}.pep.fasta' &&
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51 #else:
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52 #set $blast_path = $os.path.join($ortholog.blast_opts_ortholog.histdb.extra_files_path,'blastdb')
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53 #end if
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54
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55 ln -s '$ortholog.kobasdb' 'sqlite/${ortholog.species}.db' &&
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56
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57 #if $blast_opts.choice != 'fasta':
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58 ln -s '${blast_path}.phr' 'seq_pep/${ortholog.species}.pep.fasta.phr' &&
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59 ln -s '${blast_path}.pin' 'seq_pep/${ortholog.species}.pep.fasta.pin' &&
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60 ln -s '${blast_path}.psq' 'seq_pep/${ortholog.species}.pep.fasta.psq' &&
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61 #end if
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62 #end if
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63
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64 kobas-annotate
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65 -i '$infile'
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66 -t '$intype'
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67 -s '$species'
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68 -e '$evalue'
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69 -r $rank
3
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70 -n "\${GALAXY_SLOTS:-4}"
0
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71 -c $coverage
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72 #if $ortholog.only == 'YES':
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73 -z '$ortholog.species'
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74 #end if
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75 -y seq_pep
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76 -q sqlite
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77 -p blastp
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78 -x blastx
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79 -o '$output'
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80
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81 ]]>
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82 </command>
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83 <inputs>
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84 <param format="fasta,tabular,txt" type="data" label="Input file" help="Input data file matching the input type." argument="--infile"/>
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85 <param type="select" label="Input type" argument="--intype" help="Input data type, default fasta:pro">
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86 <option value="fasta:pro">FASTA protein sequence</option>
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87 <option value="fasta:nuc">FASTA nucleotide sequence</option>
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88 <option value="blastout:xml">XML BLAST output</option>
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89 <option value="blastout:tab">Tabular BLAST output</option>
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90 <option value="id:uniprot">UniProtKB AC</option>
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91 <option value="id:ensembl">Ensembl Gene ID</option>
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92 <option value="id:ncbigene">Entrez Gene ID</option>
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93 <option value="id:refseqpro">Refseq Protein ID</option>
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94 </param>
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95
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96 <conditional name="blast_opts">
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97 <expand macro="blastdb_selector"/>
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98 </conditional>
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99
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100 <expand macro="input_kobasdb"/>
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101
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102 <param format="sqlite" name="organismdb" type="data" label="Organism database" help="KOBAS organism database, available at http://kobas.cbi.pku.edu.cn/download.php"/>
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103 <param type="text" argument="--evalue" value="1e-5" label="E-value" help="Expect threshold for BLAST, default 1e-5"/>
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104 <param type="integer" argument="--rank" value="5" min="0" label="Rank cutoff" help="Rank cutoff for valid hits from BLAST result, default 5"/>
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105 <param type="integer" argument="--coverage" value="0" min="0" label="Subject coverage cutoff" help="subject coverage cutoff for BLAST, default 0"/>
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106 <conditional name="ortholog">
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107 <param name="only" type="select" argument="--ortholog" label="Only use orthologs" help="Whether only use orthologs for cross-species annotation or not, default NO (if only use orthologs, please provide the species abbreviation of your input)">
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108 <option value="NO">No</option>
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109 <option value="YES">Yes</option>
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110 </param>
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111 <when value="YES">
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112 <expand macro="input_kobasdb"/>
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113 <conditional name="blast_opts_ortholog">
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114 <expand macro="blastdb_selector"/>
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115 </conditional>
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116 </when>
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117 <when value="NO"></when>
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118 </conditional>
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119 </inputs>
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120 <outputs>
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121 <data format="tabular" name="output"/>
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122 </outputs>
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123
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124 <tests>
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125 <test>
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126 <param name="infile" value="kobas_annotate_input.fasta"/>
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127 <param name="intype" value="fasta:pro"/>
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128 <conditional name="blast_opts">
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129 <param name="choice" value="fasta"/>
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130 <param name="fastadb" value="aaa.pep.fasta" />
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131 </conditional>
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132 <param name="species" value="aaa"/>
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133 <param name="kobasdb" value="aaa.db"/>
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134 <param name="organismdb" value="organism.db"/>
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135 <output name="out_file1" file="kobas_annotate_output.txt"/>
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136 </test>
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137 </tests>
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138
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139 <help>
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140 @HELP_KOBAS_INFO@
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141
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142 **KOBAS Annotate**
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143
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144 Annotates an input set of genes with putative pathways and disease relationships based on mapping to genes with known annotations. It allows for both ID mapping and cross-species sequence similarity mapping.
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145
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146 @HELP_KOBAS_URL@
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147 </help>
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148
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149 <expand macro="kobas_citations"/>
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150
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151 </tool>