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annotate proteinortho.xml @ 0:4850f0d15f01 draft

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"planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
author iuc
date Tue, 18 Feb 2020 17:57:28 -0500
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children 26abc7846e6f
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4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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1 <tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>detects orthologous proteins/genes within different species</description>
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3 <macros>
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4 <import>proteinortho_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ## the following ln-action is necessary, since the file names are used by proteinortho (output contains filenames => species names)
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10 #import re
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11 #for $f in $input_files#
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12 ln -sf '$f' '${re.sub('[^\w\-_.]', '_', f.element_identifier)}' &&
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13 #end for
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14 #if $synteny.synteny_options == "specified":
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15 #for $f in $synteny.input_files_syn#
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16 ln -sf '$f' '${re.sub('[^\w\-_.]', '_', f.element_identifier)}' &&
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17 #end for#
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18 #end if
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19 proteinortho
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20 --project=result
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21 --cpus="\${GALAXY_SLOTS:-4}"
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22 --ram="\${GALAXY_MEMORY_MB:-16000}"
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23 #if $more_options.selfblast:
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24 $more_options.selfblast
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25 #end if
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26 #if $more_options.singles:
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27 $more_options.singles
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28 #end if
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29 --p=$p
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30 --e=$evalue
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31 #if $more_options.cov:
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32 --cov=$more_options.cov
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33 #end if
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34 #if $more_options.sim:
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35 --sim=`LC_NUMERIC=C awk "BEGIN {printf \"%.2f\",$more_options.sim/100}"`
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36 #end if
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37 #if $more_options.identity:
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38 --cov=$more_options.identity
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39 #end if
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40 #if $more_options.isoform != "no":
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41 --isoform=$more_options.isoform
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42 #end if
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43 #if $synteny.synteny_options == "specified":
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44 --synteny
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45 --dups=$synteny.dups
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46 --cs=$synteny.cs
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47 --alpha=$synteny.alpha
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48 #end if
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49 #for $f in $input_files#
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50 ${re.sub('[^\w\-_.]', '_', f.element_identifier)}
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51 #end for#
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52 #if $synteny.synteny_options == "specified":
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53 #for $f in $synteny.input_files_syn#
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54 ${re.sub('[^\w\-_.]', '_', f.element_identifier)}
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55 #end for#
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56 #end if
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57 2> >(sed -E "s/.\[([0-9]{1,2}(;[0-9]{1,2})?)?[mGK]//g" 1>&2)
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58 #if $synteny.synteny_options == "specified":
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59 &&
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60 mv result.poff-graph result.proteinortho-graph &&
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61 mv result.poff.tsv result.proteinortho.tsv &&
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62 mv result.poff.html result.proteinortho.html ;
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63 #end if
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64 ]]></command>
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65 <inputs>
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66 <param name="input_files" format="fasta" type="data" multiple="true" min="2" label="Select the input fasta files (>2)" help="The input fasta files. At least 2 are needed!"/>
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67 <param argument="--p" type="select" label="Similarity comparision algorithm" help="In the first step of proteinortho an all-versus-all reciprocal best hit graph is build from the input files (using this algorithm).">
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68 <option value="diamond" selected="true">diamond (aminoacid sequences)</option>
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69 <option value="autoblast">auto detect NCBI-BLAST (protein and nucleotide sequences)</option>
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70 <option value="blastp">NCBI-BLASTP+ (protein sequences)</option>
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71 <option value="blastn">NCBI-BLASTN+ (nucleotide sequences)</option>
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72 <option value="lastp">Last (aminoacid sequences)</option>
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73 <option value="lastn">Last (nucleotide sequences)</option>
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74 <option value="blatp">BLAT (aminoacid sequences)</option>
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75 <option value="blatn">BLAT (nucleotide sequences)</option>
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76 </param>
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77 <param argument="--evalue" type="float" value="0.001" min="0" label="E-value threshold of the blast algorithm" help="This is the main parameter for the generation of the reciprocal best hit graph. Larger values results in more false positives (connections between proteins)."/>
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78 <param argument="--conn" type="float" value="0.1" min="0." max="10." label="Minimal algebraic connectivity" help="This is the main parameter for the clustering step. Choose larger values then more splits are done, resulting in more and smaller clusters."/>
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79 <section name="more_options" title="Additional Options" expanded="False">
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80 <param argument="--cov" type="integer" value="50" min="0" max="100" label="Minimal coverage of best blast alignments in %"/>
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81 <param argument="--sim" type="integer" value="95" min="0" max="100" label="Minimal sequence similarity in %"/>
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82 <param argument="--identity" type="integer" value="25" min="0" max="100" label="Minimal percent identity of best blast hits in %"/>
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83 <param argument="--selfblast" type="boolean" checked="false" truevalue="--selfblast" falsevalue="" label="Apply selfblast, detects paralogs without orthologs "/>
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84 <param argument="--singles" type="boolean" checked="false" truevalue="--singles" falsevalue="" label="Report singleton genes without any hit "/>
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85 <param argument="--isoform" type="select" label="Use isoform information" help="The reciprocal best hit graph is build using isoform information (isoforms are treated equivalent). For ncbi : simply add the additional files to the input (file names need to match). For uniprot : the isoforms need to contain the word isoform and the corresponding identifier. For trinity simply use the trinity output format.">
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86 <option value="no" selected="true">Don't use isoform information</option>
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87 <option value="ncbi">ncbi style (..._additional.fasta)</option>
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88 <option value="uniprot">uniprot style (...isoform of...)</option>
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89 <option value="trinity">trinity style (...i4)</option>
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90 </param>
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91 </section>
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92 <conditional name="synteny">
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93 <param name="synteny_options" type="select" label="Activate synteny feature (POFF)" help="To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. For more details see doi:10.1371/journal.pone.0105015.">
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94 <option value="no" selected="true">no</option>
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95 <option value="specified">yes</option>
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96 </param>
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97 <when value="no"/>
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98 <when value="specified">
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99 <param argument="--dups" type="integer" value="0" min="0" max="100" label="Number of reiterations for adjacencies heuristic, to determine duplicated regions"/>
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100 <param argument="--cs" type="integer" value="3" min="0" max="100" label="Size of a maximum common substring (MCS) for adjacency matches"/>
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101 <param argument="--alpha" type="float" value="0.5" min="0." max="1." label="Minimal percent identity of best blast hits"/>
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102 <param name="input_files_syn" type="data" format="gff" multiple="true" min="2" label="Select the GFF3 files matching the input fasta files" help="The GFF3 files need matching names with the input fasta files. If you provide mybacteria123.faa or mybacteria123.fasta ... then you need to provide mybacteria123.gff here accoringly. The attributes column (#9) must contain the attribute Name=GENE IDENTIFIER where GENE IDENTIFIER corresponds to the respective (protein) identifier in the FASTA input. For example see https://gitlab.com/paulklemm_PHD/proteinortho/-/blob/master/test/C.gff"/>
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103 </when>
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104 </conditional>
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105 </inputs>
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106 <outputs>
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107 <data name="blastgraph" format="tabular" label="${tool.name} on ${on_string}: RBH graph" from_work_dir="result.blast-graph"/>
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108 <data name="proteinortho" format="tabular" label="${tool.name} on ${on_string}: orthology-groups" from_work_dir="result.proteinortho.tsv"/>
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109 <data name="proteinorthograph" format="tabular" label="${tool.name} on ${on_string}: orthology-pairs" from_work_dir="result.proteinortho-graph"/>
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110 </outputs>
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111 <tests>
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112 <test expect_num_outputs="3"> <!-- test normal -->
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113 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
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114 <output name="proteinortho">
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115 <assert_contents>
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116 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
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117 <has_text text="2&#009;5&#009;0.16"/>
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118 <has_text text="M_640,M_642,M_649"/>
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119 </assert_contents>
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120 </output>
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121 <output name="blastgraph">
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122 <assert_contents>
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123 <has_text text="L_10&#009;E_10&#009;"/>
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124 </assert_contents>
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125 </output>
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126 <output name="proteinorthograph">
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127 <assert_contents>
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128 <has_text text="L_11&#009;E_11&#009;"/>
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129 </assert_contents>
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130 </output>
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131 </test>
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132 <test expect_num_outputs="3"> <!-- various parameter -->
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133 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
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134 <param name="evalue" value="1"/>
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135 <param name="conn" value="1"/>
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136 <param name="cov" value="42"/>
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137 <param name="sim" value="42"/>
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138 <param name="identity" value="42"/>
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139 <param name="selfblast" value="true"/>
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140 <param name="singles" value="true"/>
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141 <output name="proteinortho">
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142 <assert_contents>
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143 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
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144 <has_text text="1&#009;1&#009;0"/>
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145 <has_text text="&#009;C_177&#009;"/>
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146 </assert_contents>
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147 </output>
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148 <output name="blastgraph">
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149 <assert_contents>
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150 <has_text text="C_1&#009;C_1&#009;"/>
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151 </assert_contents>
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152 </output>
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153 <output name="proteinorthograph">
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154 <assert_contents>
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155 <has_text text="C_12&#009;C_21&#009;"/>
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156 </assert_contents>
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157 </output>
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158 </test>
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159 <test expect_num_outputs="3"> <!-- synteny -->
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160 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
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161 <param name="input_files_syn" value="L.gff,C.gff,C2.gff,E.gff,M.gff"/>
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162 <param name="synteny_options" value="specified"/>
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163 <output name="proteinortho">
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164 <assert_contents>
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165 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
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166 <has_text text="4&#009;5&#009;0.144"/>
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167 <has_text text="E_313,E_315"/>
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168 </assert_contents>
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169 </output>
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170 <output name="proteinorthograph">
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171 <assert_contents>
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iuc
parents:
diff changeset
172 <has_text text="M_313&#009;L_313&#009;"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
173 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
174 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
175 </test>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
176 <test expect_num_outputs="3"> <!-- blast -->
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
177 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
178 <param name="--p" value="blastp"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
179 <output name="proteinortho">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
180 <assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
181 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
182 <has_text text="2&#009;5&#009;0.16"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
183 <has_text text="M_640,M_642,M_649"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
184 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
185 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
186 <output name="blastgraph">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
187 <assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
188 <has_text text="M_3&#009;L_3&#009;"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
189 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
190 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
191 <output name="proteinorthograph">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
192 <assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
193 <has_text text="M_317&#009;L_317&#009;"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
194 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
195 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
196 </test>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
197 <test expect_num_outputs="3"> <!-- auto blast -->
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
198 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
199 <param name="--p" value="autoblast"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
200 <output name="proteinortho">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
201 <assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
202 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
203 <has_text text="2&#009;5&#009;0.16"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
204 <has_text text="M_640,M_642,M_649"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
205 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
206 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
207 <output name="blastgraph">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
208 <assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
209 <has_text text="M_3&#009;L_3&#009;"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
210 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
211 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
212 <output name="proteinorthograph">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
213 <assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
214 <has_text text="M_317&#009;L_317&#009;"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
215 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
216 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
217 </test>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
218 <test expect_num_outputs="3"> <!-- last -->
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
219 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
220 <param name="--p" value="lastp"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
221 <output name="proteinortho">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
222 <assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
223 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
224 <has_text text="2&#009;5&#009;0.16"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
225 <has_text text="M_640,M_642,M_649"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
226 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
227 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
228 <output name="blastgraph">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
229 <assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
230 <has_text text="M_636&#009;E_317&#009;"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
231 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
232 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
233 <output name="proteinorthograph">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
234 <assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
235 <has_text text="E_11&#009;C_11&#009;"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
236 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
237 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
238 </test>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
239 <test expect_num_outputs="3"> <!-- blat -->
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
240 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
241 <param name="--p" value="blastp"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
242 <output name="proteinortho">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
243 <assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
244 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
245 <has_text text="2&#009;5&#009;0.16"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
246 <has_text text="M_640,M_642,M_649"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
247 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
248 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
249 <output name="blastgraph">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
250 <assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
251 <has_text text="E_10&#009;C_10&#009;"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
252 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
253 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
254 <output name="proteinorthograph">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
255 <assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
256 <has_text text="E_10&#009;C_10&#009;"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
257 </assert_contents>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
258 </output>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
259 </test>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
260 </tests>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
261 <help><![CDATA[Proteinortho with POFF - An orthology detection tool
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
262
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
diff changeset
263 **What it does**
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
iuc
parents:
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264
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265 Proteinortho is a tool to detect orthologous proteins/genes within different species (at least 2).
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266
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267 | It compares similarities of given gene/protein sequences and clusters them to find significant groups.
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268 | The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one.
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269 | Details can be found in (doi:10.1186/1471-2105-12-124).
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270 | To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (details see doi:10.1371/journal.pone.0105015), is already build in Proteinortho.
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271
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272 ----
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273
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274 **Proteinortho in a nutshell**
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275
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276 ----
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277
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278 * **(i) Build adaptive reciprocal best hit graph (RBH)**
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279
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280 | Using the blast algorithm (diamond,blast,blat,...) all input sequences are compared against each other.
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281 | If two proteins find each other with respect to multiple criteria like minimal evalue, similarity compared to the best hit, ... then a edge is drawn between the two proteins.
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282 | The result of this step is outputted to RBH
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283
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284 * **(ii) Cluster the RBH**
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285
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286 | Using two clustering algorithms, edges are removed that weakly connect two connected components to reduce false positive hits.
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287 | The resulting connected components are outputted in orthology-groups / -PAIRS
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288
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289 ----
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290
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291 **Proteinortho output files**
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292
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293 ----
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294
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295 * **RBH**
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296
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297 | The result of the (i) step, the reciprocal best hit graph.
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298 | First a comment line announces 2 species (# ecoli.faa human.faa), then each line corresponds to a reciprocal best hit between 2 proteins/genes of the announced species. The output format is shown below.
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299 | *seqidA*,*seqidB* = the 2 ids/names of the proteins involved
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300 | *evalue_ab* = evalue with seqidA as query and seqidB as part of the database
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301 | *bitscore_ab* = bitscore with seqidA as query ...
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302 | *evalue_ba* = evalue with seqidB as query ...
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303 | ...
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304
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305 .. csv-table::
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306
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307 seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba
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308
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309 ----
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310
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311 * **orthology-groups**
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312
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313 | The result of the (ii) step, the clustered reciprocal best hit graph or the orthology groups.
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314 | Every line corresponds to an orthology group of proteins/genes.
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315 | The first 3 columns characterize general properties of that group: number of proteins, species and the algebraic connectivity. The higher the algebraic connectivity the more edges are there and the better the group is connected to itself in general.
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316 | Then a column for each species follows containing the proteins of that species. If a species contributes with more than one protein to a group of orthologs, then they are ordered by connectivity.
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317
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318 .. csv-table::
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319
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320 Species,Genes,Alg.-Conn.
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321
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322 ----
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323
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324 * **orthology-pairs**
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325
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326 | The same as orthology-groups but every edge is printed one-by-one here. The output is formatted the same as the RBH graph:
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327
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328 .. csv-table::
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329
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330 seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba
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331
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332 ----
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333
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334 **Proteinortho-Tools for downstream analysis**
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335
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336 * `proteinortho grab proteins` : find gene(s)/protein(s) in a given fasta file and retrieve their sequence(s). You can also use a orthology-groups file.
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337 * `proteinortho summary` : Summaries the orthology-pairs/RBH files to determine how the species are connected to each other.
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338
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339 More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho
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340 ]]>
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341 </help>
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342 <expand macro="citations"/>
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343 </tool>