Mercurial > repos > iuc > proteinortho
diff proteinortho.xml @ 0:4850f0d15f01 draft
"planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2"
| author | iuc |
|---|---|
| date | Tue, 18 Feb 2020 17:57:28 -0500 |
| parents | |
| children | 26abc7846e6f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteinortho.xml Tue Feb 18 17:57:28 2020 -0500 @@ -0,0 +1,343 @@ +<tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@"> + <description>detects orthologous proteins/genes within different species</description> + <macros> + <import>proteinortho_macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ + ## the following ln-action is necessary, since the file names are used by proteinortho (output contains filenames => species names) + #import re + #for $f in $input_files# + ln -sf '$f' '${re.sub('[^\w\-_.]', '_', f.element_identifier)}' && + #end for + #if $synteny.synteny_options == "specified": + #for $f in $synteny.input_files_syn# + ln -sf '$f' '${re.sub('[^\w\-_.]', '_', f.element_identifier)}' && + #end for# + #end if + proteinortho + --project=result + --cpus="\${GALAXY_SLOTS:-4}" + --ram="\${GALAXY_MEMORY_MB:-16000}" + #if $more_options.selfblast: + $more_options.selfblast + #end if + #if $more_options.singles: + $more_options.singles + #end if + --p=$p + --e=$evalue + #if $more_options.cov: + --cov=$more_options.cov + #end if + #if $more_options.sim: + --sim=`LC_NUMERIC=C awk "BEGIN {printf \"%.2f\",$more_options.sim/100}"` + #end if + #if $more_options.identity: + --cov=$more_options.identity + #end if + #if $more_options.isoform != "no": + --isoform=$more_options.isoform + #end if + #if $synteny.synteny_options == "specified": + --synteny + --dups=$synteny.dups + --cs=$synteny.cs + --alpha=$synteny.alpha + #end if + #for $f in $input_files# + ${re.sub('[^\w\-_.]', '_', f.element_identifier)} + #end for# + #if $synteny.synteny_options == "specified": + #for $f in $synteny.input_files_syn# + ${re.sub('[^\w\-_.]', '_', f.element_identifier)} + #end for# + #end if + 2> >(sed -E "s/.\[([0-9]{1,2}(;[0-9]{1,2})?)?[mGK]//g" 1>&2) + #if $synteny.synteny_options == "specified": + && + mv result.poff-graph result.proteinortho-graph && + mv result.poff.tsv result.proteinortho.tsv && + mv result.poff.html result.proteinortho.html ; + #end if + ]]></command> + <inputs> + <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!"/> + <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)."> + <option value="diamond" selected="true">diamond (aminoacid sequences)</option> + <option value="autoblast">auto detect NCBI-BLAST (protein and nucleotide sequences)</option> + <option value="blastp">NCBI-BLASTP+ (protein sequences)</option> + <option value="blastn">NCBI-BLASTN+ (nucleotide sequences)</option> + <option value="lastp">Last (aminoacid sequences)</option> + <option value="lastn">Last (nucleotide sequences)</option> + <option value="blatp">BLAT (aminoacid sequences)</option> + <option value="blatn">BLAT (nucleotide sequences)</option> + </param> + <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)."/> + <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."/> + <section name="more_options" title="Additional Options" expanded="False"> + <param argument="--cov" type="integer" value="50" min="0" max="100" label="Minimal coverage of best blast alignments in %"/> + <param argument="--sim" type="integer" value="95" min="0" max="100" label="Minimal sequence similarity in %"/> + <param argument="--identity" type="integer" value="25" min="0" max="100" label="Minimal percent identity of best blast hits in %"/> + <param argument="--selfblast" type="boolean" checked="false" truevalue="--selfblast" falsevalue="" label="Apply selfblast, detects paralogs without orthologs "/> + <param argument="--singles" type="boolean" checked="false" truevalue="--singles" falsevalue="" label="Report singleton genes without any hit "/> + <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."> + <option value="no" selected="true">Don't use isoform information</option> + <option value="ncbi">ncbi style (..._additional.fasta)</option> + <option value="uniprot">uniprot style (...isoform of...)</option> + <option value="trinity">trinity style (...i4)</option> + </param> + </section> + <conditional name="synteny"> + <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."> + <option value="no" selected="true">no</option> + <option value="specified">yes</option> + </param> + <when value="no"/> + <when value="specified"> + <param argument="--dups" type="integer" value="0" min="0" max="100" label="Number of reiterations for adjacencies heuristic, to determine duplicated regions"/> + <param argument="--cs" type="integer" value="3" min="0" max="100" label="Size of a maximum common substring (MCS) for adjacency matches"/> + <param argument="--alpha" type="float" value="0.5" min="0." max="1." label="Minimal percent identity of best blast hits"/> + <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"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="blastgraph" format="tabular" label="${tool.name} on ${on_string}: RBH graph" from_work_dir="result.blast-graph"/> + <data name="proteinortho" format="tabular" label="${tool.name} on ${on_string}: orthology-groups" from_work_dir="result.proteinortho.tsv"/> + <data name="proteinorthograph" format="tabular" label="${tool.name} on ${on_string}: orthology-pairs" from_work_dir="result.proteinortho-graph"/> + </outputs> + <tests> + <test expect_num_outputs="3"> <!-- test normal --> + <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> + <output name="proteinortho"> + <assert_contents> + <has_text text="# Species	Genes	Alg.-Conn."/> + <has_text text="2	5	0.16"/> + <has_text text="M_640,M_642,M_649"/> + </assert_contents> + </output> + <output name="blastgraph"> + <assert_contents> + <has_text text="L_10	E_10	"/> + </assert_contents> + </output> + <output name="proteinorthograph"> + <assert_contents> + <has_text text="L_11	E_11	"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> <!-- various parameter --> + <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> + <param name="evalue" value="1"/> + <param name="conn" value="1"/> + <param name="cov" value="42"/> + <param name="sim" value="42"/> + <param name="identity" value="42"/> + <param name="selfblast" value="true"/> + <param name="singles" value="true"/> + <output name="proteinortho"> + <assert_contents> + <has_text text="# Species	Genes	Alg.-Conn."/> + <has_text text="1	1	0"/> + <has_text text="	C_177	"/> + </assert_contents> + </output> + <output name="blastgraph"> + <assert_contents> + <has_text text="C_1	C_1	"/> + </assert_contents> + </output> + <output name="proteinorthograph"> + <assert_contents> + <has_text text="C_12	C_21	"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> <!-- synteny --> + <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> + <param name="input_files_syn" value="L.gff,C.gff,C2.gff,E.gff,M.gff"/> + <param name="synteny_options" value="specified"/> + <output name="proteinortho"> + <assert_contents> + <has_text text="# Species	Genes	Alg.-Conn."/> + <has_text text="4	5	0.144"/> + <has_text text="E_313,E_315"/> + </assert_contents> + </output> + <output name="proteinorthograph"> + <assert_contents> + <has_text text="M_313	L_313	"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> <!-- blast --> + <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> + <param name="--p" value="blastp"/> + <output name="proteinortho"> + <assert_contents> + <has_text text="# Species	Genes	Alg.-Conn."/> + <has_text text="2	5	0.16"/> + <has_text text="M_640,M_642,M_649"/> + </assert_contents> + </output> + <output name="blastgraph"> + <assert_contents> + <has_text text="M_3	L_3	"/> + </assert_contents> + </output> + <output name="proteinorthograph"> + <assert_contents> + <has_text text="M_317	L_317	"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> <!-- auto blast --> + <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> + <param name="--p" value="autoblast"/> + <output name="proteinortho"> + <assert_contents> + <has_text text="# Species	Genes	Alg.-Conn."/> + <has_text text="2	5	0.16"/> + <has_text text="M_640,M_642,M_649"/> + </assert_contents> + </output> + <output name="blastgraph"> + <assert_contents> + <has_text text="M_3	L_3	"/> + </assert_contents> + </output> + <output name="proteinorthograph"> + <assert_contents> + <has_text text="M_317	L_317	"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> <!-- last --> + <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> + <param name="--p" value="lastp"/> + <output name="proteinortho"> + <assert_contents> + <has_text text="# Species	Genes	Alg.-Conn."/> + <has_text text="2	5	0.16"/> + <has_text text="M_640,M_642,M_649"/> + </assert_contents> + </output> + <output name="blastgraph"> + <assert_contents> + <has_text text="M_636	E_317	"/> + </assert_contents> + </output> + <output name="proteinorthograph"> + <assert_contents> + <has_text text="E_11	C_11	"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> <!-- blat --> + <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> + <param name="--p" value="blastp"/> + <output name="proteinortho"> + <assert_contents> + <has_text text="# Species	Genes	Alg.-Conn."/> + <has_text text="2	5	0.16"/> + <has_text text="M_640,M_642,M_649"/> + </assert_contents> + </output> + <output name="blastgraph"> + <assert_contents> + <has_text text="E_10	C_10	"/> + </assert_contents> + </output> + <output name="proteinorthograph"> + <assert_contents> + <has_text text="E_10	C_10	"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[Proteinortho with POFF - An orthology detection tool + +**What it does** + +Proteinortho is a tool to detect orthologous proteins/genes within different species (at least 2). + + | It compares similarities of given gene/protein sequences and clusters them to find significant groups. + | The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one. + | Details can be found in (doi:10.1186/1471-2105-12-124). + | 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. + +---- + +**Proteinortho in a nutshell** + +---- + +* **(i) Build adaptive reciprocal best hit graph (RBH)** + + | Using the blast algorithm (diamond,blast,blat,...) all input sequences are compared against each other. + | 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. + | The result of this step is outputted to RBH + +* **(ii) Cluster the RBH** + + | Using two clustering algorithms, edges are removed that weakly connect two connected components to reduce false positive hits. + | The resulting connected components are outputted in orthology-groups / -PAIRS + +---- + +**Proteinortho output files** + +---- + +* **RBH** + + | The result of the (i) step, the reciprocal best hit graph. + | 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. + | *seqidA*,*seqidB* = the 2 ids/names of the proteins involved + | *evalue_ab* = evalue with seqidA as query and seqidB as part of the database + | *bitscore_ab* = bitscore with seqidA as query ... + | *evalue_ba* = evalue with seqidB as query ... + | ... + +.. csv-table:: + + seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba + +---- + +* **orthology-groups** + + | The result of the (ii) step, the clustered reciprocal best hit graph or the orthology groups. + | Every line corresponds to an orthology group of proteins/genes. + | 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. + | 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. + +.. csv-table:: + + Species,Genes,Alg.-Conn. + +---- + +* **orthology-pairs** + + | The same as orthology-groups but every edge is printed one-by-one here. The output is formatted the same as the RBH graph: + +.. csv-table:: + + seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba + +---- + +**Proteinortho-Tools for downstream analysis** + +* `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. +* `proteinortho summary` : Summaries the orthology-pairs/RBH files to determine how the species are connected to each other. + +More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho +]]> + </help> + <expand macro="citations"/> +</tool>