Mercurial > repos > iuc > kobas

annotate kobas_identify.xml @ 0:e3308a2b63f4 draft

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planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
author iuc
date Fri, 04 Nov 2016 15:42:18 -0400
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children dc84c4e1f9c4
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1 <tool id="kobas_identify" name="KOBAS Identify" 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>
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6 <requirements>
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7 <requirement type="package" version="@KOBAS_VERSION@">kobas</requirement>
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8 </requirements>
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9
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10 <command>
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11 <![CDATA[
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12
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13 mkdir sqlite &&
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14 mkdir seq_pep &&
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15
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16 #if not isinstance( $db.value, list ):
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17 #set $db_args = [ $db.value ]
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18 #else:
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19 #set $db_args = $db.value
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20 #end if
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21 #set $db_args = "/".join($db.value)
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22
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23 ln -s '$kobasdb' 'sqlite/${species}.db' &&
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24
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25 kobas-identify
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26 -f '$fgfile'
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27 #if $bg.bgtype == 'file':
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28 -b '$bg.bgfile'
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29 #elif $bg.bgtype == 'species':
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30 -b '$bg.bgspecies'
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31 #end if
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32 -d '$db_args'
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33 -m '$method'
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34 -n '$fdr'
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35 -c $cutoff
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36 -q sqlite
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37 -p blastp
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38 -x blastx
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39 -o '$output'
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40 ]]>
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41 </command>
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42 <inputs>
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43 <param format="tabular" type="data" label="Foreground" argument="--fgfile" help="Foreground file, the output of KOBAS Annotate"/>
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44
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45 <expand macro="input_kobasdb"/>
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46
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47 <param type="select" label="Database" argument="--db" multiple="True" display="checkboxes" help="Select your desired databases:
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48 (Note: the Corrected P-Values will be affected by the number of selected databases)">
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49 <option value="K">KEGG Pathway</option>
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50 <option value="n">PID</option>
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51 <option value="b">BioCarta</option>
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52 <option value="R">Reactome</option>
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53 <option value="B">BioCyc</option>
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54 <option value="P">PANTHER</option>
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55 <option value="o">OMIM</option>
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56 <option value="k">KEGG Disease</option>
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57 <option value="f">FunDo</option>
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58 <option value="g">GAD</option>
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59 <option value="N">NHGRI GWAS Catalog</option>
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60 <option value="G">Gene Ontology</option>
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61 <option value="S">Gene Ontology Slim (GOslim)</option>
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62 <validator type="no_options" message="You must pick at least one database."/>
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63 </param>
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64
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65 <conditional name="bg">
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66 <param
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67 name="bgtype"
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68 type="select"
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69 argument="--bgfile"
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70 label="Background"
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71 help="Optional background file, the output of annotate (3 or 4-letter
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72 file name is not allowed), or species abbreviation
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73 (for example: hsa for Homo sapiens, mmu for Mus
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74 musculus, dme for Drosophila melanogaster, ath for
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75 Arabidopsis thaliana, sce for Saccharomyces cerevisiae
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76 and eco for Escherichia coli K-12 MG1655), default
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77 same species as annotate">
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78 <option value="same" selected="True">Same species as annotate</option>
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79 <option value="file">Background file from KOBAS Annotate</option>
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80 <option value="species">Species abbreviation</option>
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81 </param>
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82 <when value="same"></when>
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83 <when value="file">
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84 <param format="txt" name="bgfile" type="data" label="Background file"/>
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85 </when>
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86 <when value="species">
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87 <param
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88 name="bgspecies"
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89 type="text"
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90 label="Species abbreviation"
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91 help="For example: ko for KEGG
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92 Orthology, hsa for Homo sapiens, mmu for Mus musculus,
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93 dme for Drosophila melanogaster, ath for Arabidopsis
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94 thaliana, sce for Saccharomyces cerevisiae and eco for
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95 Escherichia coli K-12 MG1655"/>
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96 </when>
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97 </conditional>
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98
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99 <param argument="--method" type="select" label="Statistical test method">
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100 <option selected="True" value="h">Hpergeometric test / Fisher's exact test</option>
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101 <option value="b">Binomial test</option>
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102 <option value="c">Chi-square test</option>
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103 <option value="x">Frequency list</option>
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104 </param>
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105
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106 <param type="select" argument="--fdr" label="FDR" help="False discovery rate (FDR) correction method">
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107 <option selected="True" value="BH">Benjamini and Hochberg</option>
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108 <option value="BY">Benjamini and Yekutieli</option>
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109 <option value="QVALUE">QVALUE</option>
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110 <option value="None">None</option>
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111 </param>
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112
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113 <param type="integer" min="0" argument="--cutoff" value="5" label="Cutoff" help="Terms with less than cutoff number of genes are not used for statistical tests, default 5"/>
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114
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115 </inputs>
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116 <outputs>
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117 <data format="tabular" name="output"/>
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118 </outputs>
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119
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120 <tests>
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121 <test>
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122 <param name="fgfile" value="kobas_annotate_output.txt"/>
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123 <param name="species" value="aaa"/>
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124 <param name="kobasdb" value="aaa.db"/>
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125 <param name="db" value="K"/>
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126 <conditional name="bg">
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127 <param name="bgtype" value="same"/>
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128 </conditional>
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129 <output name="out_file1" file="kobas_identify_output.txt"/>
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130 </test>
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131 </tests>
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132
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133 <help>
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134 @HELP_KOBAS_INFO@
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135
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136 **KOBAS Identify**
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137
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138 Performs statistical tests to identify significantly enriched pathways and diseases.
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139
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140 @HELP_KOBAS_URL@
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141 </help>
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142 <expand macro="kobas_citations"/>
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143 </tool>