Mercurial > repos > iuc > proteinortho

annotate proteinortho.xml @ 5:5532c0e5d4a6 draft

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planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f
author iuc
date Fri, 16 Jun 2023 20:52:41 +0000
parents a8addd4fb60a
children 10112d9127af
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26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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1 <tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="@PROFILE@">
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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 <xml name="test_output_proteinortho" tokens="nlines">
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6 <output name="proteinortho">
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7 <metadata name="column_names" value="species,genes,alg.-conn.,L.fasta,C.fasta,E.fasta,M.fasta"/>
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8 <assert_contents>
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9 <has_n_columns n="7"/>
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10 <has_n_lines n="@NLINES@"/>
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11 <has_line_matching expression="# Species\tGenes\tAlg\.-Conn\.\t.*"/>
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12 <has_line_matching expression="[0-9]+\t[0-9]+\t.*"/>
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13 <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+.*"/>
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14 </assert_contents>
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15 </output>
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16 </xml>
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17 <xml name="test_output_blastgraph" tokens="nlines">
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18 <output name="blastgraph">
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19 <metadata name="column_names" value="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba"/>
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20 <assert_contents>
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21 <has_n_columns n="6" comment="#"/>
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22 <has_n_lines n="@NLINES@"/>
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23 <has_line_matching expression="# file_a\tfile_b"/>
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24 <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba"/>
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25 <has_line_matching expression="# (C|C2|E|L|M)\.fasta\t(C|C2|E|L|M)\.fasta"/>
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26 <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\t(C|C2|E|L|M)_[0-9]+.*"/>
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27 </assert_contents>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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28 </output>
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29 </xml>
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30 <xml name="test_output_proteinorthograph" tokens="nlines" token_nlines_delta="0" token_add_columns="" token_ncolumns="6">
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31 <output name="proteinorthograph">
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32 <metadata name="column_names" value="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba@ADD_COLUMNS@"/>
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33 <assert_contents>
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34 <has_n_columns n="@NCOLUMNS@" comment="#"/>
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35 <has_n_lines n="@NLINES@" delta="@NLINES_DELTA@"/>
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36 <has_line_matching expression="# file_a\tfile_b"/>
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37 <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba(\tsame_strand\tsimscore)?"/>
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38 <has_line_matching expression="# (C|C2|E|L|M)\.fasta\t(C|C2|E|L|M)\.fasta"/>
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39 <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\t(C|C2|E|L|M)_[0-9]+.*"/>
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40 </assert_contents>
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41 </output>
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42 </xml>
0
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43 </macros>
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44 <expand macro="requirements"/>
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45 <expand macro="version_command"/>
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46 <command detect_errors="exit_code"><![CDATA[
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47 ## the following ln-action is necessary, since the file names are used by proteinortho (output contains filenames => species names)
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48 #import re
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49 #for $f in $input_files#
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50 ln -sf '$f' '${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 $synteny.input_files_syn#
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54 ln -sf '$f' '${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 proteinortho
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58 --project=result
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59 --cpus="\${GALAXY_SLOTS:-4}"
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60 #if $more_options.selfblast:
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61 $more_options.selfblast
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62 #end if
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63 #if $more_options.singles:
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64 $more_options.singles
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65 #end if
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66 #if $more_options.core:
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67 $more_options.core
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68 #end if
0
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69 --p=$p
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70 --e=$more_options.evalue
2
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71 --conn=$conn
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72 #if $more_options.cov:
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73 --cov=$more_options.cov
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74 #end if
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75 #if $sim:
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76 --sim=`LC_NUMERIC=C awk "BEGIN {printf \"%.2f\",$sim/100}"`
0
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77 #end if
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78 #if $more_options.identity:
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79 --cov=$more_options.identity
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80 #end if
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81 #if $more_options.isoform != "no":
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82 --isoform=$more_options.isoform
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83 #end if
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84 #if $synteny.synteny_options == "specified":
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85 --synteny
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86 --dups=$synteny.dups
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87 --cs=$synteny.cs
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88 --alpha=$synteny.alpha
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89 #end if
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90 #for $f in $input_files#
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91 ${re.sub('[^\w\-_.]', '_', f.element_identifier)}
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92 #end for#
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93 #if $synteny.synteny_options == "specified":
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94 #for $f in $synteny.input_files_syn#
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95 ${re.sub('[^\w\-_.]', '_', f.element_identifier)}
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96 #end for#
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97 #end if
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98 2> >(sed -E "s/.\[([0-9]{1,2}(;[0-9]{1,2})?)?[mGK]//g" 1>&2)
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99 #if $synteny.synteny_options == "specified":
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100 &&
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101 mv result.poff-graph result.proteinortho-graph &&
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102 mv result.poff.tsv result.proteinortho.tsv &&
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103 mv result.poff.html result.proteinortho.html ;
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104 #end if
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105 ]]></command>
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106 <inputs>
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107 <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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108 <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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109 <option value="diamond" selected="true">diamond (aminoacid sequences)</option>
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110 <option value="autoblast">auto detect NCBI-BLAST (protein and nucleotide sequences)</option>
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111 <option value="blastp">NCBI-BLASTP+ (protein sequences)</option>
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112 <option value="blastn">NCBI-BLASTN+ (nucleotide sequences)</option>
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113 <option value="lastp">Last (aminoacid sequences)</option>
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114 <option value="lastn">Last (nucleotide sequences)</option>
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115 <option value="blatp">BLAT (aminoacid sequences)</option>
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116 <option value="blatn">BLAT (nucleotide sequences)</option>
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117 </param>
5
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118 <param argument="--sim" type="integer" value="95" min="0" max="100" label="Minimal reciprocal similarity in %" help="This and --evalue are main parameters for the generation of the reciprocal best hit graph. 1 = only the best reciprocal hits are reported, 0 = all possible reciprocal blast matches (within the E-value cutoff) are reported."/>
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119 <param argument="--conn" type="float" value="0.1" min="0." max="1." label="Minimal algebraic connectivity" help="This is the main parameter for the clustering step. Choose larger values than more splits are done, resulting in more and smaller clusters. A value of 0 corresponds to no clustering."/>
0
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120 <section name="more_options" title="Additional Options" expanded="False">
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121 <param argument="--evalue" type="float" value="0.001" min="0" label="E-value threshold of the blast algorithm" help="Larger values results in more false positives (connections between proteins)."/>
0
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122 <param argument="--cov" type="integer" value="50" min="0" max="100" label="Minimal coverage of best blast alignments in %"/>
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123 <param argument="--identity" type="integer" value="25" min="0" max="100" label="Minimal percent identity of best blast hits in %"/>
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124 <param argument="--selfblast" type="boolean" checked="false" truevalue="--selfblast" falsevalue="" label="Apply selfblast, detects paralogs without orthologs "/>
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125 <param argument="--singles" type="boolean" checked="false" truevalue="--singles" falsevalue="" label="Report singleton genes without any hit "/>
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126 <param argument="--core" type="boolean" checked="false" truevalue="--core" falsevalue="" label="Stop clustering if a split would result in groups that do not span across all species of the inital connected component." help="Overrules the -conn threshold."/>
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127 <param argument="--isoform" type="select" label="Use isoform information" help="The reciprocal best hit graph is built 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.">
0
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128 <option value="no" selected="true">Don't use isoform information</option>
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129 <option value="ncbi">ncbi style (..._additional.fasta)</option>
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130 <option value="uniprot">uniprot style (...isoform of...)</option>
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131 <option value="trinity">trinity style (...i4)</option>
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132 </param>
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133 </section>
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134 <conditional name="synteny">
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135 <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 an additional feature for the discrimination of orthologs. For more details see doi:10.1371/journal.pone.0105015.">
0
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136 <option value="no" selected="true">no</option>
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137 <option value="specified">yes</option>
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138 </param>
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139 <when value="no"/>
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140 <when value="specified">
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141 <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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142 <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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143 <param argument="--alpha" type="float" value="0.5" min="0." max="1." label="Weight of adjacencies vs. sequence similarity" help="alpha[FF-adj score] + (1−alpha)[BLAST score]"/>
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144 <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 accordingly. 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"/>
0
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145 </when>
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146 </conditional>
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147 </inputs>
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148 <outputs>
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149 <data name="blastgraph" format="tabular" label="${tool.name} on ${on_string}: RBH graph" from_work_dir="result.blast-graph">
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150 <actions>
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151 <action name="column_names" type="metadata"
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152 default="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba"/>
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153 </actions>
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154 </data>
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155 <data name="proteinortho" format="tabular" label="${tool.name} on ${on_string}: orthology-groups" from_work_dir="result.proteinortho.tsv">
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156 <actions>
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157 <action name="column_names" type="metadata"
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158 default="species,genes,alg.-conn.,${','.join([ f.element_identifier for f in $input_files ])}"/>
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159 </actions>
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160 </data>
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161 <data name="proteinorthograph" format="tabular" label="${tool.name} on ${on_string}: orthology-pairs" from_work_dir="result.proteinortho-graph">
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162 <actions>
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163 <conditional name="synteny.synteny_options">
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164 <when value="no">
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165 <action name="column_names" type="metadata" default="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba"/>
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166 </when>
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167 <when value="specified">
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168 <action name="column_names" type="metadata" default="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba,same_strand,simscore"/>
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169 </when>
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170 </conditional>
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171 </actions>
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172 </data>
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173 </outputs>
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174 <tests>
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175 <test expect_num_outputs="3"> <!-- test normal -->
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176 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
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177 <param name="p" value="diamond"/>
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178 <expand macro="test_output_proteinortho" nlines="34"/>
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179 <expand macro="test_output_blastgraph" nlines="157"/>
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180 <expand macro="test_output_proteinorthograph" nlines="134"/>
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181 <assert_command>
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182 <has_text text="--p=diamond"/>
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183 </assert_command>
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184 </test>
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185 <test expect_num_outputs="3"> <!-- various parameter -->
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186 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
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187 <param name="p" value="diamond"/>
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188 <param name="conn" value="1"/>
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189 <param name="sim" value="42"/>
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190 <section name="more_options">
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191 <param name="cov" value="42"/>
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192 <param name="identity" value="42"/>
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193 <param name="selfblast" value="true"/>
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194 <param name="singles" value="true"/>
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195 <param name="core" value="true"/>
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196 </section>
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197 <expand macro="test_output_proteinortho" nlines="177"/>
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198 <expand macro="test_output_blastgraph" nlines="2720"/>
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199 <expand macro="test_output_proteinorthograph" nlines="384"/>
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200 <assert_command>
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201 <has_text text="--p=diamond"/>
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202 </assert_command>
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203 </test>
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204 <test expect_num_outputs="3"> <!-- synteny -->
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205 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
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206 <param name="input_files_syn" value="L.gff,C.gff,E.gff,M.gff"/>
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207 <param name="p" value="diamond"/>
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208 <conditional name="synteny">
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209 <param name="synteny_options" value="specified"/>
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210 </conditional>
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211 <expand macro="test_output_proteinortho" nlines="38"/>
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212 <expand macro="test_output_blastgraph" nlines="157"/>
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213 <expand macro="test_output_proteinorthograph" nlines="119" nlines_delta="10" ncolumns="8" add_columns=",same_strand,simscore"/>
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214 <assert_command>
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215 <has_text text="--p=diamond"/>
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216 </assert_command>
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217 </test>
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218 <test expect_num_outputs="3"> <!-- blast -->
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219 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
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220 <param name="p" value="blastp"/>
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221 <expand macro="test_output_proteinortho" nlines="32"/>
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222 <expand macro="test_output_blastgraph" nlines="158"/>
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223 <expand macro="test_output_proteinorthograph" nlines="142"/>
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224 <assert_command>
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225 <has_text text="--p=blastp"/>
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226 </assert_command>
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227 </test>
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228 <test expect_num_outputs="3"> <!-- auto blast -->
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229 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
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230 <param name="p" value="autoblast"/>
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231 <expand macro="test_output_proteinortho" nlines="32"/>
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232 <expand macro="test_output_blastgraph" nlines="158"/>
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233 <expand macro="test_output_proteinorthograph" nlines="142"/>
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234 <assert_command>
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235 <has_text text="--p=autoblast"/>
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236 </assert_command>
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237 </test>
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238 <test expect_num_outputs="3"> <!-- last -->
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239 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
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240 <param name="p" value="lastp"/>
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241 <expand macro="test_output_proteinortho" nlines="34"/>
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242 <expand macro="test_output_blastgraph" nlines="148"/>
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243 <expand macro="test_output_proteinorthograph" nlines="133"/>
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244 <assert_command>
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245 <has_text text="--p=lastp"/>
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246 </assert_command>
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247 </test>
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248 <test expect_num_outputs="3"> <!-- blat -->
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249 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
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250 <param name="p" value="blastp"/>
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251 <expand macro="test_output_proteinortho" nlines="32"/>
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252 <expand macro="test_output_blastgraph" nlines="158"/>
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253 <expand macro="test_output_proteinorthograph" nlines="142"/>
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254 <assert_command>
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255 <has_text text="--p=blastp"/>
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256 </assert_command>
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257 </test>
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258 </tests>
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259 <help><![CDATA[Proteinortho with POFF - An orthology detection tool
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260
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261 **What it does**
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262
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263 Proteinortho is a tool to detect orthologous proteins/genes within different species (at least 2).
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264
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265 | It compares similarities of given gene/protein sequences and clusters them to find significant groups.
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266 | The algorithm was designed to handle large-scale data and can be applied to hundreds of species at once.
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267 | Details can be found in (doi:10.1186/1471-2105-12-124).
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268 | To enhance the prediction accuracy, the relative order of genes (synteny) can be used as an additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (details see doi:10.1371/journal.pone.0105015), is already built in Proteinortho.
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269
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270 ----
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271
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272 **Proteinortho in a nutshell**
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273
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274 ----
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275
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276 * **(i) Build adaptive reciprocal best hit graph (RBH)**
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277
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278 | Using the blast algorithm (diamond,blast,blat,...) all input sequences are compared against each other.
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279 | If two proteins find each other with respect to multiple criteria like minimal evalue, and similarity compared to the best hit, ... then an edge is drawn between the two proteins.
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280 | The result of this step is outputted to RBH
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281
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282 * **(ii) Cluster the RBH**
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283
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284 | Using two clustering algorithms, edges are removed that weakly connect two connected components to reduce false positive hits.
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285 | The resulting connected components are outputted in orthology-groups / -pairs
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286
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287 ----
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288
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289 **Proteinortho output files**
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290
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291 ----
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292
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293 * **RBH**
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294
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295 | The result of the (i) step, the reciprocal best hit graph.
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296 | First two comment line announces 2 species (# ecoli.faa human.faa) as well as the median values (evalue_ab,bitscore_ab,evalue_ba,bitscore_ba).
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297 | Following these header lines, each line corresponds to a reciprocal best hit of 2 proteins/genes (columns 1 and 2) of the announced species. The output format is shown below.
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298 | *seqidA*,*seqidB* = the 2 ids/names of the proteins involved
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299 | *evalue_ab* = evalue with seqidA as query and seqidB as part of the database
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300 | *bitscore_ab* = bitscore with seqidA as query ...
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301 | *evalue_ba* = evalue with seqidB as query ...
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302
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303 .. csv-table::
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304
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305 seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba
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306 # ecoli.faa,human.faa
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307 # 1.91e-112,357.5,1.825e-113,360
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308 L_10,C_10;test,4.32e-151,447,4.30e-151,446
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309 L_11,C_11,1.17e-68,209,3.00e-69,210
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310 L_14,C_14,3.64e-139,422,1.19e-142,431
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311 L_15,C_15,3.51e-100,303,2.12e-102,308
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312 L_16,C_16,3.75e-49,157,7.06e-50,159
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313 L_17,C_17,2.96e-195,578,5.50e-196,579
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314
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315 ----
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316
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317 * **orthology-groups**
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318
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319 | The result of the (ii) step, the clustered reciprocal best hit graph or the orthology groups.
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320 | Every line corresponds to an orthology group.
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321 | The first 3 columns characterize the general properties of that group: number of proteins, species, and 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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322 | Then a column for each species follows containing the proteins of these species.
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323 | If a species contributes with more than one protein to a group of orthologs, then they are ordered by descending connectivity.
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324 | The '*' represents that this species does not contribute to the group.
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325
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326 .. csv-table::
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327
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328 Species,Genes,alg.-conn.,ecoli.faa,human.faa,snail.faa,wale.faa,ebola.faa
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329 5,5,0.715,C_10,C_10;test,E_10,L_10,M_10
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330 4,6,0.115,*,C_12,E_315,L_313,M_313
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331 4,5,0.167,*,C_63,E_19,L_19,M_19
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332 4,4,0.816,*,C_64,E_18,L_18,M_18
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333
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334 ----
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335
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336 * **orthology-pairs**
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337
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338 | The same as orthology-groups but every edge is printed one-by-one instead of the whole group. The output is formatted the same as the RBH graph:
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339
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340 .. csv-table::
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341
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342 seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba
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343
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344 ----
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345
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346 **Proteinortho-Tools for downstream analysis**
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347
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348 * `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 or a subset (e.g. filter by Species>10).
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349 * `proteinortho summary` : Summaries the orthology-pairs/RBH files to determine how the species are connected to each other.
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350
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351 More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho
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352
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353 **Citations:**
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354
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355 - Lechner, Marcus, et al. "Proteinortho: detection of (co-) orthologs in large-scale analysis." BMC bioinformatics 12.1 (2011): 1-9. (10.1186/1471-2105-12-124)
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356 - Lechner, Marcus, et al. "Orthology detection combining clustering and synteny for very large datasets." PLoS one 9.8 (2014): e105015. (10.1371/journal.pone.0105015)
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357
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358 ]]>
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359 </help>
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360 <expand macro="citations" /> <!--- TODO: citations are not working in usegalxy, therefore they are added manually at the above. -->
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361 </tool>