Mercurial > repos > iuc > orthofinder_onlygroups

annotate orthofinder_only_groups.xml @ 1:918d141a166b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 649c01600172bcd42e740a0159cc91894d8e89ca
author iuc
date Sun, 03 Dec 2017 04:30:59 -0500
parents bfb20dbe1309
children 649b98adce77
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bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
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1 <tool name="OrthoFinder OnlyGroups" id="orthofinder_onlygroups" version="1.1.4">
1
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2 <description>finds orthogroups in a set of proteomes</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.4">orthofinder</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 ## prepare inputs
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9 #if $init.start=="fasta":
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10 #set $infiles = ""
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11 #for $input in $init.input_fasta
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12 ln -s '$input' '${input.element_identifier}.fasta' &&
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13 #set $infiles = $infiles + str($input.element_identifier) + ","
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14 #end for
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15 #set $infiles = $infiles[:-1]
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16 #elif $init.start=="blast":
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17 #set $infilesbl = ""
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18 #for $input in $init.input_blast_out
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19 ln -s '$input' '$input.element_identifier' &&
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20 #set $infilesbl = $infilesbl + str($input.element_identifier) + ","
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21 #end for
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22 #set $infilesbl = $infilesbl[:-1]
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24 #set $infilesfa = ""
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25 #for $input in $init.input_blast_fa
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26 ln -s '$input' '$input.element_identifier' &&
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27 #set $infilesfa = $infilesfa + str($input.element_identifier) + ","
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28 #end for
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29 #set $infilesfa = $infilesfa[:-1]
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30
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31 ln -s $init.specIDs $init.specIDs.element_identifier &&
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32 ln -s $init.seqIDs $init.seqIDs.element_identifier &&
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33 #end if
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35 ## start Orthofinder
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36 orthofinder
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37 #if $init.start=="fasta":
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38 -f .
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39 #elif $init.start=="blast":
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40 -b .
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41 #end if
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42
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43 -I $I -og -t \${GALAXY_SLOTS:-1} -a \${GALAXY_SLOTS:-1} &&
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44
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45 #if $init.start=="fasta":
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46 mv Results_* results
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47 #if $init.keepblastout=="yes":
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48 && mkdir -p results/WorkingDirectory/blast results/WorkingDirectory/fa &&
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49 mv results/WorkingDirectory/Blast* results/WorkingDirectory/blast/ &&
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50 mv results/WorkingDirectory/*.fa results/WorkingDirectory/fa/
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51 #end if
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52 #elif $init.start=="blast":
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53 mkdir results &&
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54 mv *.csv results/ &&
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55 mv Orthogroups.txt results/
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56 #end if
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57
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58 ]]>
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59 </command>
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60 <inputs>
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61 <!-- Control where Orthofinder starts -->
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62 <conditional name="init">
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63 <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder_OnlyGroups works in 2 steps. Choose 'From fasta proteomes' to run OrthoFinder_OnlyGroups from scratch and 'From blast results' if you have all the blast results from a previous OrthoFinder_OnlyGroups run.">
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64 <option value="fasta" selected="true">From fasta proteomes</option>
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65 <option value="blast">From blast results</option>
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66 </param>
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67
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68 <when value="fasta">
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69 <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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70 <param name="keepblastout" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Do you want to get the blast results ?" help="Used to re-run OrthoFinder_OnlyGroups from pre-computed blast results"/>
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71 </when>
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72
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73 <when value="blast">
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74 <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_OnlyGroups run." />
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75 <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_OnlyGroups run." />
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76 <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_OnlyGroups run."/>
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77 <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_OnlyGroups run."/>
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78 </when>
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79 </conditional>
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80
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81 <param argument="-I" type="float" value="1.5" label="Inflation parameter" help="Modify inflation parameter for MCL. Not recommended." />
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82 </inputs>
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83 <outputs>
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84 <!-- Orthogroups results -->
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85 <data format="txt" name="orthogroups1" label="Orthogroups.txt" from_work_dir="results/Orthogroups.txt" />
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86 <data format="csv" name="orthogroups2" label="Orthogroups.csv" from_work_dir="results/Orthogroups.csv" />
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87 <data format="csv" name="specs_overlap" label="Orthogroups_SpeciesOverlaps.csv" from_work_dir="results/Orthogroups_SpeciesOverlaps.csv" />
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88 <data format="csv" name="unassigned_genes" label="Orthogroups_UnassignedGenes.csv" from_work_dir="results/Orthogroups_UnassignedGenes.csv" />
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89 <data format="csv" name="stat_overall" label="Statistics_Overall.csv" from_work_dir="results/Statistics_Overall.csv" />
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90 <data format="csv" name="stat_specs" label="Statistics_PerSpecies.csv" from_work_dir="results/Statistics_PerSpecies.csv" />
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91
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92 <!-- working directory : blast outputs-->
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93 <collection name="wdblast" type="list" label="Blast_outputs">
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94 <discover_datasets pattern="__name_and_ext__" directory="results/WorkingDirectory/blast/" />
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95 <filter>init['start']=="fasta" and init['keepblastout']</filter>
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96 </collection>
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97 <collection name="wdfasta" type="list" label="Fasta_from_blast" >
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98 <discover_datasets pattern="__name_and_ext__" directory="results/WorkingDirectory/fa/" />
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99 <filter>init['start']=="fasta" and init['keepblastout']</filter>
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100 </collection>
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101 <data format="txt" name="SpeciesIDs" label="SpeciesIDs.txt" from_work_dir="results/WorkingDirectory/SpeciesIDs.txt" >
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102 <filter>init['start']=="fasta" and init['keepblastout']</filter>
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103 </data>
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104 <data format="txt" name="SequenceIDs" label="SequencesIDs.txt" from_work_dir="results/WorkingDirectory/SequenceIDs.txt" >
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105 <filter>init['start']=="fasta" and init['keepblastout']</filter>
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106 </data>
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107 </outputs>
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108 <tests>
1
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109 <!-- test orthofinder -f . -og when input files has no extension fasta/faa/fa ... -->
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110 <test>
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111 <conditional name="init">
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112 <param name="start" value="fasta" />
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113 <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" />
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114 <param name="keepblastout" value="no" />
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115 </conditional>
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116 <param name="inflation" value="1.5" />
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117 <output name="specs_overlap">
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118 <assert_contents>
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119 <has_text text="AcAcaud_trinity"/>
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120 <has_text text="AmAmphi_trinity"/>
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121 <has_text text="ApApomp_trinity"/>
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122 <has_text text="AsAsp1_trinity"/>
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123 <has_n_columns n="5"/>
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124 </assert_contents>
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125 </output>
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126 <output name="unassigned_genes">
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127 <assert_contents>
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128 <has_text text="AcAcaud_trinity"/>
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129 <has_text text="AmAmphi_trinity"/>
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130 <has_text text="ApApomp_trinity"/>
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131 <has_text text="AsAsp1_trinity"/>
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132 <has_n_columns n="5"/>
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133 </assert_contents>
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134 </output>
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135 <output name="stat_overall">
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136 <assert_contents>
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137 <has_text text="Number of genes in orthogroups"/>
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138 <has_text text="Number of unassigned genes"/>
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139 <has_text text="Percentage of orthogroups"/>
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140 <has_text text="Number of orthogroups"/>
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141 <has_text text="Number of genes"/>
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142 <has_text text="G50 (assigned genes)"/>
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143 <has_text text="G50 (all genes)"/>
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144 <has_text text="O50 (assigned genes)"/>
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145 <has_text text="O50 (all genes)"/>
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146 </assert_contents>
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147 </output>
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148 <output name="stat_specs">
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149 <assert_contents>
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150 <has_text text="AcAcaud_trinity"/>
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151 <has_text text="AmAmphi_trinity"/>
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152 <has_text text="ApApomp_trinity"/>
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153 <has_text text="AsAsp1_trinity"/>
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154 <has_text text="Number of genes per-species in orthogroup"/>
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155 <has_text text="Percentage of orthogroups"/>
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156 <has_text text="Number of orthogroups"/>
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157 <has_text text="Number of genes"/>
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158 <has_n_columns n="5"/>
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159 </assert_contents>
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160 </output>
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161 </test>
0
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162 <!-- test orthofinder -f -og -->
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163 <test>
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164 <conditional name="init">
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165 <param name="start" value="fasta" />
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166 <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" />
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167 <param name="keepblastout" value="no" />
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168 </conditional>
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169 <param name="inflation" value="1.5" />
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170 <output name="specs_overlap">
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171 <assert_contents>
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172 <has_text text="Mycoplasma_agalactiae"/>
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173 <has_text text="Mycoplasma_gallisepticum"/>
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174 <has_text text="Mycoplasma_genitalium"/>
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175 <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
176 <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
177 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
178 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
179 <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
180 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
181 <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
182 <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
183 <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
184 <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
185 <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
186 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
187 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
188 <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
189 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
190 <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
191 <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
192 <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
193 <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
194 <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
195 <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
196 <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
197 <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
198 <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
199 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
200 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
201 <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
202 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
203 <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
204 <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
205 <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
206 <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
207 <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
208 <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
209 <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
210 <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
211 <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
212 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
213 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
214 </test>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
215
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
216 <test>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
217 <conditional name="init">
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
218 <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
219 <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" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
220 <param name="keepblastout" value="yes" />
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
221 </conditional>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
222 <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
223 <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
224 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
225 <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
226 <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
227 <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
228 <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
229 <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
230 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
231 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
232 <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
233 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
234 <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
235 <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
236 <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
237 <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
238 <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
239 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
240 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
241 <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
242 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
243 <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
244 <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
245 <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
246 <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
247 <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
248 <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
249 <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
250 <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
251 <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
252 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
253 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
254 <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
255 <assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
256 <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
257 <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
258 <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
259 <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
260 <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
261 <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
262 <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
263 <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
264 <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
265 </assert_contents>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
parents:
diff changeset
266 </output>
bfb20dbe1309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f
iuc
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267 <output name="SequenceIDs" value="inputs/blastids/SequenceIDs.txt" />
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268 <output_collection name="wdfasta" type="list" count="4"/>
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269 <output_collection name="wdblast" type="list" count="16"/>
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270 </test>
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271
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272 <!-- test orthofinder -b -og -->
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273 <test>
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274 <conditional name="init">
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275 <param name="start" value="blast" />
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276 <param name="input_blast_out">
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277 <collection type="list">
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278 <element name="Blast0_0.txt" value="inputs/blastout/Blast0_0.txt"/>
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279 <element name="Blast0_1.txt" value="inputs/blastout/Blast0_1.txt"/>
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280 <element name="Blast0_2.txt" value="inputs/blastout/Blast0_2.txt"/>
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281 <element name="Blast0_3.txt" value="inputs/blastout/Blast0_3.txt"/>
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282 <element name="Blast1_0.txt" value="inputs/blastout/Blast1_0.txt"/>
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283 <element name="Blast1_1.txt" value="inputs/blastout/Blast1_1.txt"/>
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284 <element name="Blast1_2.txt" value="inputs/blastout/Blast1_2.txt"/>
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285 <element name="Blast1_3.txt" value="inputs/blastout/Blast1_3.txt"/>
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286 <element name="Blast2_0.txt" value="inputs/blastout/Blast2_0.txt"/>
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287 <element name="Blast2_1.txt" value="inputs/blastout/Blast2_1.txt"/>
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288 <element name="Blast2_2.txt" value="inputs/blastout/Blast2_2.txt"/>
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289 <element name="Blast2_3.txt" value="inputs/blastout/Blast2_3.txt"/>
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290 <element name="Blast3_0.txt" value="inputs/blastout/Blast3_0.txt"/>
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291 <element name="Blast3_1.txt" value="inputs/blastout/Blast3_1.txt"/>
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292 <element name="Blast3_2.txt" value="inputs/blastout/Blast3_2.txt"/>
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293 <element name="Blast3_3.txt" value="inputs/blastout/Blast3_3.txt"/>
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294 </collection>
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295 </param>
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296 <param name="input_blast_fa">
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297 <collection type="list">
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298 <element name="Species0.fa" value="inputs/blastfa/Species0.fa"/>
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299 <element name="Species1.fa" value="inputs/blastfa/Species1.fa"/>
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300 <element name="Species2.fa" value="inputs/blastfa/Species2.fa"/>
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301 <element name="Species3.fa" value="inputs/blastfa/Species3.fa"/>
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302 </collection>
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303 </param>
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304 <param name="specIDs" ftype="txt" value="inputs/blastids/SpeciesIDs.txt"/>
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305 <param name="seqIDs" ftype="txt" value="inputs/blastids/SequenceIDs.txt"/>
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306 </conditional>
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307 <param name="inflation" value="1.5" />
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308 <output name="orthogroups1" value="results_fromblast/Orthogroups.txt"/>
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309 <output name="orthogroups2" value="results_fromblast/Orthogroups.csv"/>
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310 <output name="specs_overlap" value="results_fromblast/Orthogroups_SpeciesOverlaps.csv"/>
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311 <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.csv"/>
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312 <output name="stat_overall" value="results_fromblast/Statistics_Overall.csv" lines_diff="2"/>
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313 <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.csv"/>
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314 </test>
1
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315 </tests>
0
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316 <help>
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317 ======================
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318 OrthoFinder OnlyGroups
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319 ======================
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320
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321 Full readme at https://github.com/davidemms/OrthoFinder/blob/master/README.md
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322 Summary sketch at https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-options.pdf
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323
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324 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).
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325
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326 .. class:: infomark
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327
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328 This galaxy tool implements the first part of the Orthofinder program, e.g. the clustering of orthogroups of genes.
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329
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330 If you have already ran OrthoFinder, the tool allows to re-run the analysis from the pre-computed blast-results.
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331
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332 -----------
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333 Input files
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334 -----------
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335 - 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.
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336 - 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):
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337 - A dataset collection / multiple datasets for the blast outputs
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338 - A dataset collection / multiple datasets for .fa files
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339 - The SpeciesIDs.txt file
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340 - The SequencesIDs.txt file
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341
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342 </help>
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343 <citations>
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344 <citation type="doi">10.1186/s13059-015-0721-2</citation>
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345 </citations>
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346 </tool>