annotate orthofinder_only_groups.xml @ 5:974d8c28e586 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
author iuc
date Mon, 17 Aug 2020 12:59:19 -0400
parents 999060f051ac
children 0ff17c7a18cd
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1 <tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@">
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2 <description>finds orthogroups in a set of proteomes</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 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement>
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8 <requirement type="package" version="2.34">util-linux</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import re
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12 ## prepare inputs
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13 #if $init.start == "fasta":
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14 #set $infiles = ""
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15 #for $input in $init.input_fasta
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16 #set $identifier=re.sub('[^\w\-\s\.]', '_', str($input.element_identifier))
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17 ln -s '$input' '${identifier}.fasta' &&
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18 #set $infiles = $infiles + str($identifier) + ","
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19 #end for
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20 #set $infiles = $infiles[:-1]
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21 #elif $init.start == "blast":
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22 #set $infilesbl = ""
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23 #for $input in $init.input_blast_out
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24 #set $identifier=re.sub('[^\w\-\s\.]', '_', str($input.element_identifier))
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25 ln -s '$input' '$identifier' &&
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26 #set $infilesbl = $infilesbl + str($identifier) + ","
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27 #end for
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28 #set $infilesbl = $infilesbl[:-1]
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29
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30 #set $infilesfa = ""
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31 #for $input in $init.input_blast_fa
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32 #set $identifier=re.sub('[^\w\-\s\.]', '_', str($input.element_identifier))
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33 ln -s '$input' '$identifier' &&
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34 #set $infilesfa = $infilesfa + str($identifier) + ","
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35 #end for
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36 #set $infilesfa = $infilesfa[:-1]
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37
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38 #set $identifier=re.sub('[^\w\-\s\.]', '_', str($init.specIDs.element_identifier))
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39 ln -s $init.specIDs $identifier &&
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40
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41 #set $identifier=re.sub('[^\w\-\s\.]', '_', str($init.seqIDs.element_identifier))
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42 ln -s $init.seqIDs $identifier &&
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43 #end if
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44
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45 ## start Orthofinder
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46 orthofinder
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47 #if $init.start == "fasta":
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48 -f .
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49 -S $init.search.search_program
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50 #elif $init.start == "blast":
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51 -b .
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52 #end if
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53
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54 -I $I
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55
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56 #if $trees.run_mode == "full":
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57 -M '${trees.tree_method.method}'
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58 #if $trees.tree_method.method == "msa":
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59 -A '${trees.tree_method.msa_program}'
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60 -T '${trees.tree_method.msa_tree_program}'
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61 #end if
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62 #else:
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63 $trees.run_mode
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64 #end if
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65
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66 -t \${GALAXY_SLOTS:-1} -a \${GALAXY_SLOTS:-1} &&
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67
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68 mv OrthoFinder/Results_* results
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69 #if $init.start == "fasta":
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70 #if $init.search.search_program == "blast":
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71 #if $init.search.keepblastout:
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72 && mkdir -p results/WorkingDirectory/blast results/WorkingDirectory/fa &&
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73 mv results/WorkingDirectory/Blast* results/WorkingDirectory/blast/ &&
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74 mv results/WorkingDirectory/*.fa results/WorkingDirectory/fa/
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75 #end if
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76 #end if
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77 #end if
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78 ]]></command>
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79 <inputs>
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80 <!-- Control where Orthofinder starts -->
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81 <conditional name="init">
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82 <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder can be run in 2 steps. Choose 'From fasta proteomes' to run OrthoFinder from scratch or 'From blast results' if you have all the blast results from a previous OrthoFinder run.">
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83 <option value="fasta" selected="true">From fasta proteomes</option>
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84 <option value="blast">From blast results</option>
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85 </param>
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86
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87 <when value="fasta">
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88 <param name="input_fasta" type="data" format="fasta" multiple="true" label="Select input fasta proteomes" help="One fasta file per species; species and sequences names in the results will remain the same than in the input files."/>
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89 <conditional name="search">
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90 <param name="search_program" type="select" label="Sequence search program">
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91 <option value="diamond" selected="true">Diamond (faster)</option>
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92 <option value="blast">Blast</option>
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93 <option value="blast_gz">Blast_gz - blast results gzipped</option>
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94 </param>
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95 <when value="blast">
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96 <param name="keepblastout" type="boolean" checked="true" label="Do you want to get the blast results?" help="Used to re-run OrthoFinder from pre-computed blast results"/>
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97 </when>
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98 <when value="diamond"></when>
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99 <when value="blast_gz"></when>
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100 </conditional>
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101 </when>
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102
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103 <when value="blast">
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104 <param name="input_blast_out" type="data_collection" collection_type="list" format="txt" label="Select the pre-computed blast files" help="blastX_Y.txt files from the blast output files of a previous OrthoFinder run." />
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105 <param name="input_blast_fa" type="data_collection" collection_type="list" format="fasta" label="Select the fasta files" help="= SpeciesX.fa files from the blast output files of a previous OrthoFinder run." />
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106 <param name="specIDs" type="data" format="txt" label="Select the SpeciesIds file" help="SpeciesIDs.txt file from the blast output files of a previous OrthoFinder run."/>
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107 <param name="seqIDs" type="data" format="txt" label="Select the SequencesIds file" help="SequencesIDs.txt file from the blast output files of a previous OrthoFinder run."/>
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108 </when>
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109 </conditional>
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110
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111 <conditional name="trees">
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112 <param name="run_mode" type="select" label="Orthofinder run mode">
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113 <option value="full" selected="true">Full run (including gene trees)</option>
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114 <option value="-og">Stop after inferring orthogroups (no gene trees)</option>
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115 </param>
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116
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117 <when value="full">
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118 <conditional name="tree_method">
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119 <param name="method" type="select" label="Method for gene tree inference">
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120 <option value="dendroblast" selected="true">Dendroblast (faster)</option>
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121 <option value="msa">MSA (Multiple Sequence Aligments)</option>
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122 </param>
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123
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124 <when value="msa">
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125 <param name="msa_program" type="select" label="MSA program">
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126 <option value="mafft" selected="true">Mafft</option>
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127 <option value="muscle">Muscle</option>
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128 </param>
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129 <param name="msa_tree_program" type="select" label="Tree inference method">
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130 <option value="fasttree" selected="true">FastTree (recommended)</option>
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131 <option value="raxml">raxml</option>
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132 <option value="raxml-ng">raxml-ng</option>
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133 <option value="iqtree">iqtree</option>
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134 </param>
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135 </when>
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136
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137 <when value="dendroblast"/>
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138 </conditional>
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139 </when>
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140
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141 <when value="-og"/>
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142 </conditional>
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143
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144 <param argument="-I" type="float" value="1.5" label="Inflation parameter" help="Modify inflation parameter for MCL. Not recommended." />
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145 <param name="output_duplications" type="boolean" checked="false" label="Generate output about gene duplication events"/>
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146 </inputs>
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147 <outputs>
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148 <!-- Orthogroups results -->
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149 <data format="txt" name="orthogroups1" label="OrthoFinder on ${on_string}: orthogroups (txt)" from_work_dir="results/Orthogroups/Orthogroups.txt" />
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150 <data format="tsv" name="orthogroups2" label="OrthoFinder on ${on_string}: orthogroups (tsv)" from_work_dir="results/Orthogroups/Orthogroups.tsv" />
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151 <data format="tsv" name="specs_overlap" label="OrthoFinder on ${on_string}: species overlaps" from_work_dir="results/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv" />
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152 <data format="tsv" name="unassigned_genes" label="OrthoFinder on ${on_string}: unassigned genes" from_work_dir="results/Orthogroups/Orthogroups_UnassignedGenes.tsv" />
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153 <data format="tsv" name="stat_overall" label="OrthoFinder on ${on_string}: overall comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_Overall.tsv" />
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154 <data format="tsv" name="stat_specs" label="OrthoFinder on ${on_string}: per species comparative genomics statistics" from_work_dir="results/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv" />
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155
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156 <!-- working directory : blast outputs-->
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157 <collection name="wdblast" type="list" label="OrthoFinder on ${on_string}: blast outputs">
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158 <discover_datasets pattern="__name_and_ext__" directory="results/WorkingDirectory/blast" />
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159 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
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160 </collection>
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161 <collection name="wdfasta" type="list" label="OrthoFinder on ${on_string}: fasta from blast" >
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162 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fa" directory="results/WorkingDirectory/fa" format="fasta" />
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163 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
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164 </collection>
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165 <data format="txt" name="SpeciesIDs" label="OrthoFinder on ${on_string}: SpeciesIDs" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" >
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166 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']"</filter>
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167 </data>
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168 <data format="txt" name="SequenceIDs" label="OrthoFinder on ${on_string}: SequencesIDs" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" >
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169 <filter>init['start'] == "fasta" and init['search']['search_program'] == "blast" and init['search']['keepblastout']</filter>
0
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170 </data>
5
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171
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172 <data format="newick" name="species_tree" label="OrthoFinder on ${on_string}: species tree" from_work_dir="results/Species_Tree/SpeciesTree_rooted.txt">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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173 <filter>trees['run_mode'] == "full"</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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174 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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175 <data format="newick" name="species_tree_label" label="OrthoFinder on ${on_string}: species tree with node labels" from_work_dir="results/Species_Tree/SpeciesTree_rooted_node_labels.txt">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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176 <filter>trees['run_mode'] == "full"</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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177 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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178 <collection name="genetrees" type="list" label="OrthoFinder on ${on_string}: gene trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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179 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="results/Gene_Trees" format="newick" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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180 <filter>trees['run_mode'] == "full"</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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181 </collection>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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182
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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183 <data format="newick" name="species_tree_duplications" label="OrthoFinder on ${on_string}: species tree with duplication events" from_work_dir="results/Gene_Duplication_Events/SpeciesTree_Gene_Duplications_0.5_Support.txt">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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184 <filter>trees['run_mode'] == "full" and output_duplications</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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185 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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186 <data format="tsv" name="duplications" label="OrthoFinder on ${on_string}: duplication events" from_work_dir="results/Gene_Duplication_Events/Duplications.tsv">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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187 <filter>trees['run_mode'] == "full" and output_duplications</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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188 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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189 <data format="tsv" name="duplications_per_orthogroup" label="OrthoFinder on ${on_string}: duplications per orthogroup" from_work_dir="results/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
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190 <filter>trees['run_mode'] == "full" and output_duplications</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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191 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
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192 <data format="tsv" name="duplications_per_species_tree_node" label="OrthoFinder on ${on_string}: duplications per species tree node" from_work_dir="results/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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193 <filter>trees['run_mode'] == "full" and output_duplications</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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194 </data>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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195 <collection name="resolved_trees" type="list" label="OrthoFinder on ${on_string}: resolved gene trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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196 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="results/Resolved_Gene_Trees" format="newick" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
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diff changeset
197 <filter>trees['run_mode'] == "full" and output_duplications</filter>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
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198 </collection>
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
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199 </outputs>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
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200 <tests>
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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201 <!-- no trees + diamond + input files have no extension fasta/faa/fa -->
1
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202 <test>
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iuc
parents: 0
diff changeset
203 <conditional name="init">
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
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204 <param name="start" value="fasta" />
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
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205 <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" />
2
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
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206 <conditional name="search">
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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207 <param name="search_program" value="diamond"/>
2
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
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208 </conditional>
1
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
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209 </conditional>
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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210 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
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211 <param name="run_mode" value="-og" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
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212 </conditional>
1
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iuc
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213 <param name="inflation" value="1.5" />
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iuc
parents: 0
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214 <output name="specs_overlap">
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
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215 <assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
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216 <has_text text="AcAcaud_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
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217 <has_text text="AmAmphi_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
218 <has_text text="ApApomp_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
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219 <has_text text="AsAsp1_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
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220 <has_n_columns n="5"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
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221 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
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222 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
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223 <output name="unassigned_genes">
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
224 <assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
225 <has_text text="AcAcaud_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
226 <has_text text="AmAmphi_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
227 <has_text text="ApApomp_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
228 <has_text text="AsAsp1_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
229 <has_n_columns n="5"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
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230 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
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231 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
232 <output name="stat_overall">
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
233 <assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
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234 <has_text text="Number of genes in orthogroups"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
235 <has_text text="Number of unassigned genes"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
236 <has_text text="Percentage of orthogroups"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
237 <has_text text="Number of orthogroups"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
238 <has_text text="Number of genes"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
239 <has_text text="G50 (assigned genes)"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
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240 <has_text text="G50 (all genes)"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
241 <has_text text="O50 (assigned genes)"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
242 <has_text text="O50 (all genes)"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
243 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
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diff changeset
244 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
245 <output name="stat_specs">
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
246 <assert_contents>
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iuc
parents: 0
diff changeset
247 <has_text text="AcAcaud_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
248 <has_text text="AmAmphi_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
249 <has_text text="ApApomp_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
250 <has_text text="AsAsp1_trinity"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
251 <has_text text="Number of genes per-species in orthogroup"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
252 <has_text text="Percentage of orthogroups"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
253 <has_text text="Number of orthogroups"/>
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iuc
parents: 0
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254 <has_text text="Number of genes"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
255 <has_n_columns n="5"/>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
256 </assert_contents>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
257 </output>
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
258 </test>
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
259 <!-- no trees + diamond + input files have extension fasta/faa/fa -->
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
260 <test>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
261 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
262 <param name="start" value="fasta" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
263 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
2
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
264 <conditional name="search">
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
265 <param name="search_program" value="diamond"/>
2
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
266 </conditional>
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
267 </conditional>
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
268 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
269 <param name="run_mode" value="-og" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
270 </conditional>
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
271 <param name="inflation" value="1.5" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
272 <output name="specs_overlap">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
273 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
274 <has_text text="Mycoplasma_agalactiae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
275 <has_text text="Mycoplasma_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
276 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
277 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
278 <has_n_columns n="5"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
279 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
280 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
281 <output name="unassigned_genes">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
282 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
283 <has_text text="Mycoplasma_agalactiae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
284 <has_text text="Mycoplasma_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
285 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
286 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
287 <has_n_columns n="5"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
288 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
289 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
290 <output name="stat_overall">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
291 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
292 <has_text text="Number of genes in orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
293 <has_text text="Number of unassigned genes"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
294 <has_text text="Percentage of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
295 <has_text text="Number of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
296 <has_text text="Number of genes"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
297 <has_text text="G50 (assigned genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
298 <has_text text="G50 (all genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
299 <has_text text="O50 (assigned genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
300 <has_text text="O50 (all genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
301 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
302 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
303 <output name="stat_specs">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
304 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
305 <has_text text="Mycoplasma_agalactiae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
306 <has_text text="Mycoplasma_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
307 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
308 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
309 <has_text text="Number of genes per-species in orthogroup"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
310 <has_text text="Percentage of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
311 <has_text text="Number of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
312 <has_text text="Number of genes"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
313 <has_n_columns n="5"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
314 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
315 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
316 </test>
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
317 <!-- no trees + diamond + input files have extension fasta/faa/fa + keep blast out -->
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
318 <test>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
319 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
320 <param name="start" value="fasta" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
321 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
2
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
322 <conditional name="search">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
323 <param name="search_program" value="blast"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
324 <param name="keepblastout" value="true" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
325 </conditional>
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
326 </conditional>
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
327 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
328 <param name="run_mode" value="-og" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
329 </conditional>
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
330 <param name="inflation" value="1.5" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
331 <output name="specs_overlap">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
332 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
333 <has_text text="Mycoplasma_agalactiae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
334 <has_text text="Mycoplasma_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
335 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
336 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
337 <has_n_columns n="5"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
338 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
339 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
340 <output name="unassigned_genes">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
341 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
342 <has_text text="Mycoplasma_agalactiae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
343 <has_text text="Mycoplasma_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
344 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
345 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
346 <has_n_columns n="5"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
347 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
348 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
349 <output name="stat_overall">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
350 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
351 <has_text text="Number of genes in orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
352 <has_text text="Number of unassigned genes"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
353 <has_text text="Percentage of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
354 <has_text text="Number of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
355 <has_text text="Number of genes"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
356 <has_text text="G50 (assigned genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
357 <has_text text="G50 (all genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
358 <has_text text="O50 (assigned genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
359 <has_text text="O50 (all genes)"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
360 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
361 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
362 <output name="stat_specs">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
363 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
364 <has_text text="Mycoplasma_agalactiae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
365 <has_text text="Mycoplasma_gallisepticum"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
366 <has_text text="Mycoplasma_genitalium"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
367 <has_text text="Mycoplasma_hyopneumoniae"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
368 <has_text text="Number of genes per-species in orthogroup"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
369 <has_text text="Percentage of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
370 <has_text text="Number of orthogroups"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
371 <has_text text="Number of genes"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
372 <has_n_columns n="5"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
373 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
374 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
375 <output name="SequenceIDs" value="inputs/blastids/SequenceIDs.txt" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
376 <output_collection name="wdfasta" type="list" count="4"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
377 <output_collection name="wdblast" type="list" count="16"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
378 </test>
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
379 <!-- no trees + blast + input files have extension fasta/faa/fa-->
2
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
380 <test>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
381 <conditional name="init">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
382 <param name="start" value="fasta" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
383 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
384 <conditional name="search">
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
385 <param name="search_program" value="blast"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
386 <param name="keepblastout" value="false" />
2
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
387 </conditional>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
388 </conditional>
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
389 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
390 <param name="run_mode" value="-og" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
391 </conditional>
2
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
392 <param name="inflation" value="1.5" />
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
393 <output name="specs_overlap">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
394 <assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
395 <has_text text="Mycoplasma_agalactiae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
396 <has_text text="Mycoplasma_gallisepticum"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
397 <has_text text="Mycoplasma_genitalium"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
398 <has_text text="Mycoplasma_hyopneumoniae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
399 <has_n_columns n="5"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
400 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
401 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
402 <output name="unassigned_genes">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
403 <assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
404 <has_text text="Mycoplasma_agalactiae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
405 <has_text text="Mycoplasma_gallisepticum"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
406 <has_text text="Mycoplasma_genitalium"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
407 <has_text text="Mycoplasma_hyopneumoniae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
408 <has_n_columns n="5"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
409 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
410 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
411 <output name="stat_overall">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
412 <assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
413 <has_text text="Number of genes in orthogroups"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
414 <has_text text="Number of unassigned genes"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
415 <has_text text="Percentage of orthogroups"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
416 <has_text text="Number of orthogroups"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
417 <has_text text="Number of genes"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
418 <has_text text="G50 (assigned genes)"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
419 <has_text text="G50 (all genes)"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
420 <has_text text="O50 (assigned genes)"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
421 <has_text text="O50 (all genes)"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
422 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
423 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
424 <output name="stat_specs">
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
425 <assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
426 <has_text text="Mycoplasma_agalactiae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
427 <has_text text="Mycoplasma_gallisepticum"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
428 <has_text text="Mycoplasma_genitalium"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
429 <has_text text="Mycoplasma_hyopneumoniae"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
430 <has_text text="Number of genes per-species in orthogroup"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
431 <has_text text="Percentage of orthogroups"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
432 <has_text text="Number of orthogroups"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
433 <has_text text="Number of genes"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
434 <has_n_columns n="5"/>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
435 </assert_contents>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
436 </output>
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
437 </test>
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
438 <!-- no trees + uploaded blast-->
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
439 <test>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
440 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
441 <param name="start" value="blast" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
442 <param name="input_blast_out">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
443 <collection type="list">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
444 <element name="Blast0_0.txt" value="inputs/blastout/Blast0_0.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
445 <element name="Blast0_1.txt" value="inputs/blastout/Blast0_1.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
446 <element name="Blast0_2.txt" value="inputs/blastout/Blast0_2.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
447 <element name="Blast0_3.txt" value="inputs/blastout/Blast0_3.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
448 <element name="Blast1_0.txt" value="inputs/blastout/Blast1_0.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
449 <element name="Blast1_1.txt" value="inputs/blastout/Blast1_1.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
450 <element name="Blast1_2.txt" value="inputs/blastout/Blast1_2.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
451 <element name="Blast1_3.txt" value="inputs/blastout/Blast1_3.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
452 <element name="Blast2_0.txt" value="inputs/blastout/Blast2_0.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
453 <element name="Blast2_1.txt" value="inputs/blastout/Blast2_1.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
454 <element name="Blast2_2.txt" value="inputs/blastout/Blast2_2.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
455 <element name="Blast2_3.txt" value="inputs/blastout/Blast2_3.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
456 <element name="Blast3_0.txt" value="inputs/blastout/Blast3_0.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
457 <element name="Blast3_1.txt" value="inputs/blastout/Blast3_1.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
458 <element name="Blast3_2.txt" value="inputs/blastout/Blast3_2.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
459 <element name="Blast3_3.txt" value="inputs/blastout/Blast3_3.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
460 </collection>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
461 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
462 <param name="input_blast_fa">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
463 <collection type="list">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
464 <element name="Species0.fa" value="inputs/blastfa/Species0.fa"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
465 <element name="Species1.fa" value="inputs/blastfa/Species1.fa"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
466 <element name="Species2.fa" value="inputs/blastfa/Species2.fa"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
467 <element name="Species3.fa" value="inputs/blastfa/Species3.fa"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
468 </collection>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
469 </param>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
470 <param name="specIDs" ftype="txt" value="inputs/blastids/SpeciesIDs.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
471 <param name="seqIDs" ftype="txt" value="inputs/blastids/SequenceIDs.txt"/>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
472 </conditional>
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
473 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
474 <param name="run_mode" value="-og" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
475 </conditional>
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
476 <param name="inflation" value="1.5" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
477 <output name="orthogroups1" value="results_fromblast/Orthogroups.txt"/>
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
478 <output name="orthogroups2" value="results_fromblast/Orthogroups.tsv"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
479 <output name="specs_overlap" value="results_fromblast/Orthogroups_SpeciesOverlaps.tsv"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
480 <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.tsv"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
481 <output name="stat_overall" value="results_fromblast/Statistics_Overall.tsv" lines_diff="2"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
482 <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.tsv"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
483 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
484 <!-- full mode + diamond + input files have extension fasta/faa/fa -->
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
485 <test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
486 <conditional name="init">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
487 <param name="start" value="fasta" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
488 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
489 <conditional name="search">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
490 <param name="search_program" value="diamond"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
491 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
492 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
493 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
494 <param name="run_mode" value="full" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
495 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
496 <param name="inflation" value="1.5" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
497 <output name="specs_overlap">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
498 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
499 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
500 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
501 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
502 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
503 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
504 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
505 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
506 <output name="unassigned_genes">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
507 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
508 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
509 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
510 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
511 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
512 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
513 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
514 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
515 <output name="stat_overall">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
516 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
517 <has_text text="Number of genes in orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
518 <has_text text="Number of unassigned genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
519 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
520 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
521 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
522 <has_text text="G50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
523 <has_text text="G50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
524 <has_text text="O50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
525 <has_text text="O50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
526 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
527 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
528 <output name="stat_specs">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
529 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
530 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
531 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
532 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
533 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
534 <has_text text="Number of genes per-species in orthogroup"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
535 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
536 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
537 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
538 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
539 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
540 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
541 <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
542 <output_collection name="genetrees" type="list" count="0"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
543 <output_collection name="resolved_trees" type="list" count="0"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
544 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
545 <!-- full mode + diamond + input files have extension fasta/faa/fa + duplications -->
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
546 <test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
547 <conditional name="init">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
548 <param name="start" value="fasta" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
549 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
550 <conditional name="search">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
551 <param name="search_program" value="diamond"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
552 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
553 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
554 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
555 <param name="run_mode" value="full" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
556 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
557 <param name="inflation" value="1.5" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
558 <param name="output_duplications" value="true" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
559 <output name="specs_overlap">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
560 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
561 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
562 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
563 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
564 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
565 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
566 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
567 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
568 <output name="unassigned_genes">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
569 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
570 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
571 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
572 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
573 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
574 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
575 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
576 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
577 <output name="stat_overall">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
578 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
579 <has_text text="Number of genes in orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
580 <has_text text="Number of unassigned genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
581 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
582 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
583 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
584 <has_text text="G50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
585 <has_text text="G50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
586 <has_text text="O50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
587 <has_text text="O50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
588 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
589 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
590 <output name="stat_specs">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
591 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
592 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
593 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
594 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
595 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
596 <has_text text="Number of genes per-species in orthogroup"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
597 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
598 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
599 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
600 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
601 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
602 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
603 <output name="species_tree" value="results/SpeciesTree_rooted.txt" compare="sim_size"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
604 <output name="species_tree_duplications" value="results/SpeciesTree_Gene_Duplications_0.5_Support.txt" compare="sim_size"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
605 <output name="duplications" value="results/Duplications.tsv" compare="sim_size"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
606 <output name="duplications_per_orthogroup" value="results/Duplications_per_Orthogroup.tsv" compare="sim_size"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
607 <output name="duplications_per_species_tree_node" value="results/Duplications_per_Species_Tree_Node.tsv" compare="sim_size"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
608 <output_collection name="genetrees" type="list" count="325"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
609 <output_collection name="resolved_trees" type="list" count="325"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
610 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
611 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
612 <test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
613 <conditional name="init">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
614 <param name="start" value="fasta" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
615 <param name="input_fasta" ftype="fasta" value="inputs/no_fa_ext/AcAcaud_trinity,inputs/no_fa_ext/AmAmphi_trinity,inputs/no_fa_ext/ApApomp_trinity,inputs/no_fa_ext/AsAsp1_trinity" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
616 <conditional name="search">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
617 <param name="search_program" value="diamond"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
618 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
619 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
620 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
621 <param name="run_mode" value="-og" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
622 <conditional name="tree_method">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
623 <param name="method" value="msa" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
624 <param name="msa_program" value="muscle" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
625 <param name="msa_tree_program" value="raxml" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
626 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
627 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
628 <param name="inflation" value="1.5" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
629 <output name="specs_overlap">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
630 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
631 <has_text text="AcAcaud_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
632 <has_text text="AmAmphi_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
633 <has_text text="ApApomp_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
634 <has_text text="AsAsp1_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
635 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
636 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
637 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
638 <output name="unassigned_genes">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
639 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
640 <has_text text="AcAcaud_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
641 <has_text text="AmAmphi_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
642 <has_text text="ApApomp_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
643 <has_text text="AsAsp1_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
644 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
645 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
646 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
647 <output name="stat_overall">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
648 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
649 <has_text text="Number of genes in orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
650 <has_text text="Number of unassigned genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
651 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
652 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
653 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
654 <has_text text="G50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
655 <has_text text="G50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
656 <has_text text="O50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
657 <has_text text="O50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
658 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
659 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
660 <output name="stat_specs">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
661 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
662 <has_text text="AcAcaud_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
663 <has_text text="AmAmphi_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
664 <has_text text="ApApomp_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
665 <has_text text="AsAsp1_trinity"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
666 <has_text text="Number of genes per-species in orthogroup"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
667 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
668 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
669 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
670 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
671 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
672 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
673 </test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
674 <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
675 <test>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
676 <conditional name="init">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
677 <param name="start" value="fasta" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
678 <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
679 <conditional name="search">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
680 <param name="search_program" value="diamond"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
681 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
682 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
683 <conditional name="trees">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
684 <param name="run_mode" value="full" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
685 <conditional name="tree_method">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
686 <param name="method" value="msa" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
687 <param name="msa_program" value="muscle" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
688 <param name="msa_tree_program" value="raxml" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
689 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
690 </conditional>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
691 <param name="inflation" value="1.5" />
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
692 <output name="specs_overlap">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
693 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
694 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
695 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
696 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
697 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
698 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
699 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
700 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
701 <output name="unassigned_genes">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
702 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
703 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
704 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
705 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
706 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
707 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
708 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
709 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
710 <output name="stat_overall">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
711 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
712 <has_text text="Number of genes in orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
713 <has_text text="Number of unassigned genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
714 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
715 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
716 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
717 <has_text text="G50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
718 <has_text text="G50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
719 <has_text text="O50 (assigned genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
720 <has_text text="O50 (all genes)"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
721 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
722 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
723 <output name="stat_specs">
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
724 <assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
725 <has_text text="Mycoplasma_agalactiae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
726 <has_text text="Mycoplasma_gallisepticum"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
727 <has_text text="Mycoplasma_genitalium"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
728 <has_text text="Mycoplasma_hyopneumoniae"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
729 <has_text text="Number of genes per-species in orthogroup"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
730 <has_text text="Percentage of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
731 <has_text text="Number of orthogroups"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
732 <has_text text="Number of genes"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
733 <has_n_columns n="5"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
734 </assert_contents>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
735 </output>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
736 <assert_command>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
737 <has_text text="-M 'msa'"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
738 <has_text text="-A 'muscle'"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
739 <has_text text="-T 'raxml'"/>
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
740 </assert_command>
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
741 </test>
1
918d141a166b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
iuc
parents: 0
diff changeset
742 </tests>
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
743 <help>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
744 ======================
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
745 OrthoFinder OnlyGroups
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
746 ======================
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
747
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
748 Full readme at https://github.com/davidemms/OrthoFinder/blob/master/README.md
3
1aed170afb2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit c39323361ef6ba2664646e4476736c80bcd01124"
iuc
parents: 2
diff changeset
749 Summary sketch at https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
750
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
751 OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format (Emms, D.M. and Kelly, S., 2015).
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
752
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
753 .. class:: infomark
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
754
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
755 This galaxy tool implements the first part of the Orthofinder program, e.g. the clustering of orthogroups of genes.
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
756
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
757 If you have already ran OrthoFinder, the tool allows to re-run the analysis from the pre-computed blast-results.
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
758
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
759 -----------
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
760 Input files
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
761 -----------
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
762 - When using "from fasta" option (e.g Orthofinder from scratch) : the input files are a set of proteomes in fasta format (on file per species). Choose this option if you have no OrthoFinder results yet.
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
763 - When using "from blast results" option : the input files are all the following files from of a previous OrthoFinder run (these files appear only if you have chosen to keep them while launching a previous run):
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
764 - A dataset collection / multiple datasets for the blast outputs
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
765 - A dataset collection / multiple datasets for .fa files
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
766 - The SpeciesIDs.txt file
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
767 - The SequencesIDs.txt file
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
768
2
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
769 ----------
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
770 Parameters
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
771 ----------
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
772 - Sequence search program : You can choose either blast, blast_gz, or diamond (diamond is faster)
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
773 - Get the blast results : Check "Yes" if, while using blast as the sequence search program, you want to retrieve the blast output files
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
774 - Inflation : the inflation parameter; modify this parameter is not recommended.
649b98adce77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 297228981612581ddd4588e042141a5b12fc7840
iuc
parents: 1
diff changeset
775
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
776 </help>
5
974d8c28e586 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c"
iuc
parents: 4
diff changeset
777 <expand macro="citations"/>
0
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
778 </tool>