Mercurial > repos > iuc > kobas

annotate kobas_identify.xml @ 4:20f1b45dea63 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kobas commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 15:50:07 -0500
parents 83b998fa34ea
children
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1 <tool id="kobas_identify" name="KOBAS Identify" version="@TOOL_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
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9 <command><![CDATA[
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10 mkdir sqlite &&
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11 mkdir seq_pep &&
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12
4
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13 #if not isinstance( $db.value, list ):
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14 #set $db_args = [ $db.value ]
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15 #else:
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16 #set $db_args = $db.value
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17 #end if
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18 #set $db_args = "/".join($db.value)
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19
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20 ln -s '$kobasdb' 'sqlite/${species}.db' &&
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21
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22 kobas-identify
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23 -f '$fgfile'
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24 #if $bg.bgtype == 'file':
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25 -b '$bg.bgfile'
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26 #elif $bg.bgtype == 'species':
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27 -b '$bg.bgspecies'
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28 #end if
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29 -d '$db_args'
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30 -m '$method'
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31 -n '$fdr'
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32 -c $cutoff
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33 -q sqlite
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34 -p blastp
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35 -x blastx
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36 -o '$output'
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37 ]]></command>
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38 <inputs>
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39 <param argument="--fgfile" type="data" format="tabular" label="Foreground" help="Foreground file, the output of KOBAS Annotate"/>
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40
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41 <expand macro="input_kobasdb"/>
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42
4
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43 <param type="select" label="Database" argument="--db" multiple="True" optional="false" display="checkboxes" help="Select your desired databases:
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44 (Note: the Corrected P-Values will be affected by the number of selected databases)">
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45 <option value="K">KEGG Pathway</option>
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46 <option value="n">PID</option>
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47 <option value="b">BioCarta</option>
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48 <option value="R">Reactome</option>
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49 <option value="B">BioCyc</option>
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50 <option value="P">PANTHER</option>
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51 <option value="o">OMIM</option>
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52 <option value="k">KEGG Disease</option>
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53 <option value="f">FunDo</option>
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54 <option value="g">GAD</option>
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55 <option value="N">NHGRI GWAS Catalog</option>
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56 <option value="G">Gene Ontology</option>
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57 <option value="S">Gene Ontology Slim (GOslim)</option>
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58 </param>
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59
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60 <conditional name="bg">
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61 <param name="bgtype" argument="--bgfile" type="select" label="Background"
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62 help="Optional background file, the output of annotate (3 or 4-letter
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63 file name is not allowed), or species abbreviation
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64 (for example: hsa for Homo sapiens, mmu for Mus
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65 musculus, dme for Drosophila melanogaster, ath for
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66 Arabidopsis thaliana, sce for Saccharomyces cerevisiae
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67 and eco for Escherichia coli K-12 MG1655), default
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68 same species as annotate">
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69 <option value="same" selected="True">Same species as annotate</option>
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70 <option value="file">Background file from KOBAS Annotate</option>
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71 <option value="species">Species abbreviation</option>
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72 </param>
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73 <when value="same"></when>
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74 <when value="file">
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75 <param name="bgfile" type="data" format="txt" label="Background file"/>
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76 </when>
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77 <when value="species">
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78 <param name="bgspecies" type="text" label="Species abbreviation"
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79 help="For example: ko for KEGG
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80 Orthology, hsa for Homo sapiens, mmu for Mus musculus,
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81 dme for Drosophila melanogaster, ath for Arabidopsis
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82 thaliana, sce for Saccharomyces cerevisiae and eco for
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83 Escherichia coli K-12 MG1655"/>
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84 </when>
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85 </conditional>
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86
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87 <param argument="--method" type="select" label="Statistical test method">
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88 <option selected="True" value="h">Hpergeometric test / Fisher's exact test</option>
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89 <option value="b">Binomial test</option>
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90 <option value="c">Chi-square test</option>
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91 <option value="x">Frequency list</option>
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92 </param>
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93
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94 <param argument="--fdr" type="select" label="FDR" help="False discovery rate (FDR) correction method">
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95 <option selected="True" value="BH">Benjamini and Hochberg</option>
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96 <option value="BY">Benjamini and Yekutieli</option>
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97 <option value="QVALUE">QVALUE</option>
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98 <option value="None">None</option>
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99 </param>
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100
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101 <param argument="--cutoff" type="integer" min="0" 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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102 </inputs>
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103 <outputs>
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104 <data name="output" format="tabular"/>
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105 </outputs>
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106
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107 <tests>
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108 <test>
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109 <param name="fgfile" value="kobas_annotate_output.txt"/>
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110 <param name="species" value="aaa"/>
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111 <param name="kobasdb" value="aaa.db"/>
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112 <param name="db" value="K"/>
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113 <conditional name="bg">
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114 <param name="bgtype" value="same"/>
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115 </conditional>
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20f1b45dea63 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kobas commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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116 <output name="output" file="kobas_identify_output.txt"/>
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117 </test>
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118 </tests>
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119
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120 <help>
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121 @HELP_KOBAS_INFO@
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122
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123 **KOBAS Identify**
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124
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125 Performs statistical tests to identify significantly enriched pathways and diseases.
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126
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127 @HELP_KOBAS_URL@
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128 </help>
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129 <expand macro="kobas_citations"/>
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130 </tool>