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1 <tool id="plant_tribes_gene_family_integrator" name="GeneFamilyIntegrator" version="@WRAPPER_VERSION@.0">
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2 <description>integrates gene models in pre-computed orthologous gene family clusters with classified gene coding sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements_gene_family_integrator" />
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 #set input_format = $input_format_cond.input_format
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10 #set scaffold = $input_format_cond.scaffold
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11 #set method = $input_format_cond.method
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12
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13 python $__tool_directory__/gene_family_integrator.py
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14 --scaffold '$scaffold.fields.path'
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15 --method $method
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16 #if str($input_format) == 'ptortho':
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17 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
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18 --output '$output_ptortho'
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19 --output_dir '$output_ptortho.files_path'
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20 #else:
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21 ## str($input_format) == 'ptorthocs'
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22 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
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23 #if str($input_format_cond.orthogroup_fna) == 'yes':
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24 --orthogroup_fna 'true'
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25 --output '$output_ptorthocs'
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26 --output_dir '$output_ptorthocs.files_path'
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27 #else:
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28 --output '$output_ptortho'
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29 --output_dir '$output_ptortho.files_path'
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30 #end if
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31 #end if
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32 ]]>
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33 </command>
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34 <inputs>
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35 <conditional name="input_format_cond">
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36 <param name="input_format" type="select" label="Classified orthogroup fasta files">
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37 <option value="ptortho">Proteins orthogroup fasta files</option>
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38 <option value="ptorthocs">Protein and coding sequences orthogroup fasta files</option>
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39 </param>
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40 <when value="ptortho">
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41 <param name="input_ptortho" format="ptortho" type="data" label="Proteins orthogroup fasta files">
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42 <validator type="empty_extra_files_path" />
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43 </param>
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44 <expand macro="param_scaffold" />
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45 <expand macro="param_method" />
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46 </when>
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47 <when value="ptorthocs">
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48 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Protein and coding sequences orthogroup fasta files">
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49 <validator type="empty_extra_files_path" />
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50 </param>
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51 <expand macro="param_scaffold" />
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52 <expand macro="param_method" />
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53 <expand macro="param_orthogroup_fna" />
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54 </when>
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55 </conditional>
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56 </inputs>
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57 <outputs>
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58 <data name="output_ptortho" format="ptortho" label="${tool.name} (integrated gene family clusters) on ${on_string}">
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59 <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter>
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60 </data>
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61 <data name="output_ptorthocs" format="ptorthocs" label="${tool.name} (integrated gene family clusters) on ${on_string}">
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62 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter>
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63 </data>
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="input_format" value="ptorthocs"/>
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68 <param name="input_ptorthocs" value="input.ptorthocs" ftype="ptorthocs"/>
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69 <param name="scaffold" value="22Gv1.1"/>
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70 <param name="method" value="orthomcl"/>
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71 <param name="classifier" value="both"/>
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72 <param name="orthogroup_fna" value="yes"/>
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73 <output name="output_ptorthocs" file="output.ptorthocs" ftype="ptorthocs"/>
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74 </test>
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75 </tests>
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76 <help>
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77 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
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78 analyses of genome-scale gene families and transcriptomes. This tool integrates PlantTribes scaffold orthogroup backbone
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79 gene models with gene coding sequences classified into the scaffold by the GeneFamilyClassifier tool.
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80
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81 -----
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82
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83 **Required options**
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84
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85 * **Classified orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyClassifier tool selected from your history. Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences.
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86
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87 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds installed into Galaxy by the PlantTribes Scaffold Data Manager tool.
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88 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool.
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89
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90 **Other options**
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91
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92 * **Orthogroups coding sequences** - Select 'Yes' to create corresponding coding sequences orthogroup fasta files for the classified protein sequences.
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93
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94 </help>
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95 <citations>
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96 <expand macro="citation1" />
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97 <citation type="bibtex">
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98 @article{Wall2008,
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99 journal = {Nucleic Acids Research},
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100 author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
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101 title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
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102 year = {2008},
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103 volume = {36},
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104 number = {suppl 1},
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105 pages = {D970-D976},}
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106 </citation>
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107 <citation type="bibtex">
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108 @article{Sasidharan2012,
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109 journal = {Nucleic Acids Research},
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110 author = {3. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
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111 title = {GFam: a platform for automatic annotation of gene families},
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112 year = {2012},
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113 pages = {gks631},}
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114 </citation>
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115 <citation type="bibtex">
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116 @article{Li2003,
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117 journal = {Genome Research}
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118 author = {4. Li L, Stoeckert CJ, Roos DS},
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119 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
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120 year = {2003},
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121 volume = {13},
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122 number = {9},
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123 pages = {2178-2189},}
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124 </citation>
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125 <citation type="bibtex">
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126 @article{Emms2015,
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127 journal = {Genome Biology}
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128 author = {5. Emms DM, Kelly S},
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129 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
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130 year = {2015},
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131 volume = {16},
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132 number = {1},
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133 pages = {157},}
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134 </citation>
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135 </citations>
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136 </tool>
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