Mercurial > repos > iuc > proteinortho

annotate proteinortho.xml @ 2:a8addd4fb60a draft

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"planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit e3b372fc401662aa541a893024c65aa645f5e8cf"
author iuc
date Sat, 27 Nov 2021 09:53:00 +0000
parents 26abc7846e6f
children 5532c0e5d4a6
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1
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
iuc
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1 <tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="@PROFILE@">
0
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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>
1
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
iuc
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5 <xml name="test_outputs">
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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6 <output name="proteinortho">
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7 <assert_contents>
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8 <has_line_matching expression="# Species\tGenes\tAlg\.-Conn\.\t.*"/>
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9 <has_line_matching expression="[0-9]+\t[0-9]+\t.*"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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10 <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+.*"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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11 </assert_contents>
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12 </output>
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13 <output name="blastgraph">
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14 <assert_contents>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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15 <has_line_matching expression="# file_a\tfile_b"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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16 <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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17 <has_line_matching expression="# (C|C2|E|L|M)\.fasta\t(C|C2|E|L|M)\.fasta"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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18 <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\t(C|C2|E|L|M)_[0-9]+.*"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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19 </assert_contents>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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20 </output>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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21 <output name="proteinorthograph">
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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22 <assert_contents>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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23 <has_line_matching expression="# file_a\tfile_b"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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24 <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba(\tsame_strand\tsimscore)?"/>
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25 <has_line_matching expression="# (C|C2|E|L|M)\.fasta\t(C|C2|E|L|M)\.fasta"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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26 <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\t(C|C2|E|L|M)_[0-9]+.*"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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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>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
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29 </xml>
0
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30 </macros>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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31 <expand macro="requirements"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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32 <expand macro="version_command"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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33 <command detect_errors="exit_code"><![CDATA[
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34 ## the following ln-action is necessary, since the file names are used by proteinortho (output contains filenames => species names)
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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35 #import re
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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36 #for $f in $input_files#
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37 ln -sf '$f' '${re.sub('[^\w\-_.]', '_', f.element_identifier)}' &&
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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38 #end for
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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39 #if $synteny.synteny_options == "specified":
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
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40 #for $f in $synteny.input_files_syn#
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41 ln -sf '$f' '${re.sub('[^\w\-_.]', '_', f.element_identifier)}' &&
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42 #end for#
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43 #end if
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44 proteinortho
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45 --project=result
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46 --cpus="\${GALAXY_SLOTS:-4}"
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47 --ram="\${GALAXY_MEMORY_MB:-16000}"
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48 #if $more_options.selfblast:
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49 $more_options.selfblast
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50 #end if
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51 #if $more_options.singles:
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52 $more_options.singles
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53 #end if
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54 --p=$p
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55 --e=$evalue
2
a8addd4fb60a "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit e3b372fc401662aa541a893024c65aa645f5e8cf"
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56 --conn=$conn
0
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57 #if $more_options.cov:
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58 --cov=$more_options.cov
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59 #end if
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60 #if $more_options.sim:
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61 --sim=`LC_NUMERIC=C awk "BEGIN {printf \"%.2f\",$more_options.sim/100}"`
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62 #end if
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63 #if $more_options.identity:
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64 --cov=$more_options.identity
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65 #end if
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66 #if $more_options.isoform != "no":
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67 --isoform=$more_options.isoform
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68 #end if
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69 #if $synteny.synteny_options == "specified":
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70 --synteny
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71 --dups=$synteny.dups
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72 --cs=$synteny.cs
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73 --alpha=$synteny.alpha
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74 #end if
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75 #for $f in $input_files#
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76 ${re.sub('[^\w\-_.]', '_', f.element_identifier)}
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77 #end for#
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78 #if $synteny.synteny_options == "specified":
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79 #for $f in $synteny.input_files_syn#
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80 ${re.sub('[^\w\-_.]', '_', f.element_identifier)}
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81 #end for#
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82 #end if
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83 2> >(sed -E "s/.\[([0-9]{1,2}(;[0-9]{1,2})?)?[mGK]//g" 1>&2)
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84 #if $synteny.synteny_options == "specified":
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85 &&
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86 mv result.poff-graph result.proteinortho-graph &&
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87 mv result.poff.tsv result.proteinortho.tsv &&
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88 mv result.poff.html result.proteinortho.html ;
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89 #end if
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90 ]]></command>
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91 <inputs>
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92 <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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93 <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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94 <option value="diamond" selected="true">diamond (aminoacid sequences)</option>
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95 <option value="autoblast">auto detect NCBI-BLAST (protein and nucleotide sequences)</option>
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96 <option value="blastp">NCBI-BLASTP+ (protein sequences)</option>
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97 <option value="blastn">NCBI-BLASTN+ (nucleotide sequences)</option>
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98 <option value="lastp">Last (aminoacid sequences)</option>
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99 <option value="lastn">Last (nucleotide sequences)</option>
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100 <option value="blatp">BLAT (aminoacid sequences)</option>
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101 <option value="blatn">BLAT (nucleotide sequences)</option>
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102 </param>
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103 <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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104 <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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105 <section name="more_options" title="Additional Options" expanded="False">
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106 <param argument="--cov" type="integer" value="50" min="0" max="100" label="Minimal coverage of best blast alignments in %"/>
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107 <param argument="--sim" type="integer" value="95" min="0" max="100" label="Minimal sequence similarity in %"/>
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108 <param argument="--identity" type="integer" value="25" min="0" max="100" label="Minimal percent identity of best blast hits in %"/>
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109 <param argument="--selfblast" type="boolean" checked="false" truevalue="--selfblast" falsevalue="" label="Apply selfblast, detects paralogs without orthologs "/>
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110 <param argument="--singles" type="boolean" checked="false" truevalue="--singles" falsevalue="" label="Report singleton genes without any hit "/>
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111 <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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112 <option value="no" selected="true">Don't use isoform information</option>
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113 <option value="ncbi">ncbi style (..._additional.fasta)</option>
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114 <option value="uniprot">uniprot style (...isoform of...)</option>
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115 <option value="trinity">trinity style (...i4)</option>
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116 </param>
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117 </section>
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118 <conditional name="synteny">
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119 <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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120 <option value="no" selected="true">no</option>
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121 <option value="specified">yes</option>
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122 </param>
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123 <when value="no"/>
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124 <when value="specified">
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125 <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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126 <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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127 <param argument="--alpha" type="float" value="0.5" min="0." max="1." label="Minimal percent identity of best blast hits"/>
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128 <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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129 </when>
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130 </conditional>
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131 </inputs>
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132 <outputs>
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133 <data name="blastgraph" format="tabular" label="${tool.name} on ${on_string}: RBH graph" from_work_dir="result.blast-graph"/>
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134 <data name="proteinortho" format="tabular" label="${tool.name} on ${on_string}: orthology-groups" from_work_dir="result.proteinortho.tsv"/>
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135 <data name="proteinorthograph" format="tabular" label="${tool.name} on ${on_string}: orthology-pairs" from_work_dir="result.proteinortho-graph"/>
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136 </outputs>
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137 <tests>
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138 <test expect_num_outputs="3"> <!-- test normal -->
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139 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
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140 <expand macro="test_outputs"/>
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141 <assert_command>
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142 <has_text text="--p=diamond"/>
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143 </assert_command>
0
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144 </test>
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145 <test expect_num_outputs="3"> <!-- various parameter -->
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146 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
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147 <param name="evalue" value="1"/>
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148 <param name="conn" value="1"/>
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149 <param name="cov" value="42"/>
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150 <param name="sim" value="42"/>
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151 <param name="identity" value="42"/>
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152 <param name="selfblast" value="true"/>
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153 <param name="singles" value="true"/>
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154 <expand macro="test_outputs"/>
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155 <assert_command>
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156 <has_text text="--p=diamond"/>
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157 </assert_command>
0
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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 <expand macro="test_outputs"/>
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164 <assert_command>
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165 <has_text text="--p=diamond"/>
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166 </assert_command>
0
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167 </test>
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168 <test expect_num_outputs="3"> <!-- blast -->
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169 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
1
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170 <param name="p" value="blastp"/>
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171 <expand macro="test_outputs"/>
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172 <assert_command>
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173 <has_text text="--p=blastp"/>
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174 </assert_command>
0
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175 </test>
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176 <test expect_num_outputs="3"> <!-- auto blast -->
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177 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
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178 <param name="p" value="autoblast"/>
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179 <expand macro="test_outputs"/>
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180 <assert_command>
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181 <has_text text="--p=autoblast"/>
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182 </assert_command>
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183 </test>
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184 <test expect_num_outputs="3"> <!-- last -->
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185 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
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186 <param name="p" value="lastp"/>
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187 <expand macro="test_outputs"/>
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188 <assert_command>
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189 <has_text text="--p=lastp"/>
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190 </assert_command>
0
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191 </test>
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192 <test expect_num_outputs="3"> <!-- blat -->
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193 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
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194 <param name="p" value="blastp"/>
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195 <expand macro="test_outputs"/>
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196 <assert_command>
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197 <has_text text="--p=blastp"/>
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198 </assert_command>
0
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199 </test>
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200 </tests>
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201 <help><![CDATA[Proteinortho with POFF - An orthology detection tool
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202
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203 **What it does**
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204
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205 Proteinortho is a tool to detect orthologous proteins/genes within different species (at least 2).
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206
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207 | It compares similarities of given gene/protein sequences and clusters them to find significant groups.
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208 | The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one.
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209 | Details can be found in (doi:10.1186/1471-2105-12-124).
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210 | 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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211
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212 ----
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213
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214 **Proteinortho in a nutshell**
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215
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216 ----
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217
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218 * **(i) Build adaptive reciprocal best hit graph (RBH)**
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219
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220 | Using the blast algorithm (diamond,blast,blat,...) all input sequences are compared against each other.
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221 | 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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222 | The result of this step is outputted to RBH
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223
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224 * **(ii) Cluster the RBH**
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225
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226 | Using two clustering algorithms, edges are removed that weakly connect two connected components to reduce false positive hits.
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227 | The resulting connected components are outputted in orthology-groups / -PAIRS
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228
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229 ----
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230
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231 **Proteinortho output files**
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232
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233 ----
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234
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235 * **RBH**
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236
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237 | The result of the (i) step, the reciprocal best hit graph.
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238 | 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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239 | *seqidA*,*seqidB* = the 2 ids/names of the proteins involved
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240 | *evalue_ab* = evalue with seqidA as query and seqidB as part of the database
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241 | *bitscore_ab* = bitscore with seqidA as query ...
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242 | *evalue_ba* = evalue with seqidB as query ...
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243 | ...
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244
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245 .. csv-table::
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246
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247 seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba
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248
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249 ----
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250
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251 * **orthology-groups**
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252
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253 | The result of the (ii) step, the clustered reciprocal best hit graph or the orthology groups.
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254 | Every line corresponds to an orthology group of proteins/genes.
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255 | 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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256 | 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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257
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258 .. csv-table::
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259
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260 Species,Genes,Alg.-Conn.
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261
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262 ----
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263
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264 * **orthology-pairs**
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265
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266 | 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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267
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268 .. csv-table::
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269
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270 seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba
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271
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272 ----
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273
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274 **Proteinortho-Tools for downstream analysis**
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275
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276 * `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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277 * `proteinortho summary` : Summaries the orthology-pairs/RBH files to determine how the species are connected to each other.
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278
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279 More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho
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280 ]]>
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281 </help>
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282 <expand macro="citations"/>
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283 </tool>