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