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1 <tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="1.0.0">
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0
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2 <description>pipeline</description>
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3 <requirements>
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4 <requirement type="package" version="0.2">plant_tribes_gene_family_classifier</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <exit_code range="1:" />
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9 <!-- In case the return code has not been set properly check stderr too -->
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10 <regex match="Error:" />
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11 <regex match="Exception:" />
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12 </stdio>
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13 <command>
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14 <![CDATA[
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4
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15 #if str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
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16 #set orthogroups_fasta_dir = $options_type.create_orthogroup_cond.coding_sequences.extra_files_path
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5
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17 mkdir -p $orthogroups_fasta_dir &&
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4
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18 #end if
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0
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19 GeneFamilyClassifier
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20 --proteins "$input"
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21 --scaffold "$scaffold"
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22 --method $method
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23 --classifier $classifier
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24 #if str($options_type.options_type_selector) == 'advanced':
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25 --super_orthogroups $options_type.super_orthogroups
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26 #if str($options_type.single_copy_cond) == 'taxa':
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27 --single_copy_taxa $options_type.single_copy_cond.single_copy_taxa
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28 --taxa_present $options_type.single_copy_cond.taxa_present
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29 #end if
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3
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30 #if str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
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31 --orthogroup_fasta
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32 --coding_sequences "$options_type.create_orthogroup_cond.coding_sequences"
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33 #end if
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34 #end if
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2
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35 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
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36 --num_threads \${GALAXY_SLOTS:-4}
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4
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37 #if str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
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7
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38 && cp "./geneFamilyClassification_dir/orthogroups_fasta/*" $orthogroups_fasta_dir
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4
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39 #end if
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0
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40 ]]>
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41 </command>
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42 <inputs>
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43 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/>
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44 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
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45 <options from_data_table="plant_tribes_scaffolds" />
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46 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/>
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47 </param>
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48 <param name="method" type="select" label="Protein clustering method">
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49 <option value="gfam" selected="true">GFam</option>
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50 <option value="orthofinder">OrthoFinder</option>
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51 <option value="orthomcl">OrthoMCL</option>
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52 </param>
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53 <param name="classifier" type="select" label="Protein classification method">
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54 <option value="blastp" selected="true">blastp</option>
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55 <option value="hmmscan">HMMScan</option>
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56 <option value="both">Both blastp and HMMScan</option>
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57 </param>
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58 <conditional name="options_type">
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59 <param name="options_type_selector" type="select" label="Options Configuration">
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60 <option value="basic" selected="true">Basic</option>
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61 <option value="advanced">Advanced</option>
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62 </param>
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63 <when value="basic" />
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64 <when value="advanced">
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65 <param name="super_orthogroups" type="select" label="SuperOrthogroups MCL clustering" help="blastp e-value matrix between all pairs of orthogroups">
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66 <option value="min_evalue" selected="true">Minimum e-value</option>
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67 <option value="avg_evalue">Average e-value</option>
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68 </param>
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69 <conditional name="single_copy_cond">
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70 <param name="single_copy" type="select" label="Select single copy configuration">
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71 <option value="custom" selected="true">Single copy orthogroup custom</option>
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72 <option value="taxa">Minumum single copy taxa required in orthogroup</option>
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73 </param>
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74 <when value="custom" />
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75 <when value="taxa">
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76 <param name="single_copy_taxa" type="integer" value="20" label="Minumum single copy taxa required in orthogroup"/>
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77 <param name="taxa_present" type="integer" value="21" label="Minumum taxa required in single copy orthogroup"/>
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78 </when>
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79 </conditional>
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80 <conditional name="create_orthogroup_cond">
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81 <param name="create_orthogroup" type="select" label="Create orthogroup fasta files?">
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82 <option value="no" selected="true">No</option>
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83 <option value="yes">Yes</option>
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84 </param>
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85 <when value="no" />
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86 <when value="yes">
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87 <param name="coding_sequences" format="fasta" type="data" label="Corresponding coding sequences (CDS) fasta file"/>
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88 </when>
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89 </conditional>
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90 </when>
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91 </conditional>
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92 </inputs>
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93 <outputs>
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94 <collection name="transcripts" type="list">
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1
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95 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="true" ext="fasta" />
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0
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96 </collection>
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97 </outputs>
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98 <tests>
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99 <test>
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100 <param name="input" value="" ftype="fasta" />
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101 <param name="prediction_method" value="transdecoder"/>
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102 <param name="target_gene_family_assembly" value="no"/>
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103 <param name="strand_specific" value="yes"/>
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104 <param name="dereplicate" value="yes"/>
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105 <param name="min_length" value="200"/>
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106 <output_collection name="orthos" type="list">
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107
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108 </output_collection>
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109 </test>
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110 </tests>
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111 <help>
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112 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
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113 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs Gene family
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114 classification of the post processed de novo transcripts using either blastp (faster), HMMScan (slower but more sensitive to remote
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115 homologs) or both (more exhaustive).
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116
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117 -----
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118
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119 **Options**
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120
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121 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
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122 * **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL.
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123 * **Protein classification method** - One of blastp, HMMScan or both.
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124 * **SuperOrthogroups MCL clustering** - blastp e-value matrix between all pairs of orthogroups.
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125 * **Minumum single copy taxa required in orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
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126 * **Minumum taxa required in single copy orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
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127 * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?".
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128
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129 </help>
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130 <citations>
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131 <citation type="bibtex">
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132 @unpublished{None,
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133 author = {None},
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134 title = {None},
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135 year = {None},
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136 eprint = {None},
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137 url = {None}
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138 }</citation>
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139 </citations>
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140 </tool>
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