comparison proteinortho.xml @ 7:c5dd4f86d981 draft

planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 5eba1fb52a5ec1e63ca126be42062323e1a76687

6:10112d9127af

<tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>detects orthologous proteins/genes within different species</description>
    <macros>
        <import>proteinortho_macros.xml</import>
        <xml name="test_output_proteinortho" tokens="nlines">
            <output name="proteinortho">
                <metadata name="column_names" value="species,genes,alg.-conn.,L.fasta,C.fasta,E.fasta,M.fasta"/>
                <assert_contents>
                    <has_n_columns n="7"/>
                    <has_n_lines n="@NLINES@"/>
                    <has_line_matching expression="# Species\tGenes\tAlg\.-Conn\.\t.*"/>
                    <has_line_matching expression="[0-9]+\t[0-9]+\t.*"/>
                    <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+.*"/>
                </assert_contents>
            </output>
        </xml>
        <xml name="test_output_blastgraph" tokens="nlines">
            <output name="blastgraph">
                <metadata name="column_names" value="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba"/>
                <assert_contents>
                    <has_n_columns n="6" comment="#"/>
                    <has_n_lines n="@NLINES@"/>
                    <has_line_matching expression="# file_a\tfile_b"/>
                    <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba"/>
                    <has_line_matching expression="# (C|C2|E|L|M)\.fasta\t(C|C2|E|L|M)\.fasta"/>
                    <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\t(C|C2|E|L|M)_[0-9]+.*"/>
                </assert_contents>

                #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 ;

    </outputs>
    <tests>
        <test expect_num_outputs="3"> <!-- test normal -->
            <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
            <param name="p" value="diamond"/>
            <expand macro="test_output_proteinortho" nlines="34"/>
            <expand macro="test_output_blastgraph" nlines="157"/>
            <expand macro="test_output_proteinorthograph" nlines="134"/>
            <assert_command>
                <has_text text="--p=diamond"/>
            </assert_command>
        </test>
        <test expect_num_outputs="3"> <!-- various parameter -->

            <param name="conn" value="1"/>
            <param name="sim" value="42"/>
            <section name="more_options">
                <param name="cov" value="42"/>
                <param name="identity" value="42"/>
                <param name="selfblast" value="true"/>
                <param name="singles" value="true"/>
                <param name="core" value="true"/>
            </section>
            <expand macro="test_output_proteinortho" nlines="177"/>
            <expand macro="test_output_blastgraph" nlines="2720"/>
            <expand macro="test_output_proteinorthograph" nlines="384"/>
            <assert_command>
                <has_text text="--p=diamond"/>
            </assert_command>
        </test>
        <test expect_num_outputs="3"> <!-- synteny -->

            <param name="input_files_syn" value="L.gff,C.gff,E.gff,M.gff"/>
            <param name="p" value="diamond"/>
            <conditional name="synteny">
                <param name="synteny_options" value="specified"/>
            </conditional>
            <expand macro="test_output_proteinortho" nlines="38"/>
            <expand macro="test_output_blastgraph" nlines="157"/>
            <expand macro="test_output_proteinorthograph" nlines="119" nlines_delta="10" ncolumns="8" add_columns=",same_strand,simscore"/>
            <assert_command>
                <has_text text="--p=diamond"/>
            </assert_command>
        </test>
        <test expect_num_outputs="3"> <!-- blast -->
            <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
            <param name="p" value="blastp"/>
            <expand macro="test_output_proteinortho" nlines="32"/>
            <expand macro="test_output_blastgraph" nlines="158"/>
            <expand macro="test_output_proteinorthograph" nlines="142"/>
            <assert_command>
                <has_text text="--p=blastp"/>
            </assert_command>
        </test>
        <test expect_num_outputs="3"> <!-- auto blast -->
            <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
            <param name="p" value="autoblast"/>
            <expand macro="test_output_proteinortho" nlines="32"/>
            <expand macro="test_output_blastgraph" nlines="158"/>
            <expand macro="test_output_proteinorthograph" nlines="142"/>
            <assert_command>
                <has_text text="--p=autoblast"/>
            </assert_command>
        </test>
        <test expect_num_outputs="3"> <!-- last -->
            <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
            <param name="p" value="lastp"/>
            <expand macro="test_output_proteinortho" nlines="34"/>
            <expand macro="test_output_blastgraph" nlines="148"/>
            <expand macro="test_output_proteinorthograph" nlines="133"/>
            <assert_command>
                <has_text text="--p=lastp"/>
            </assert_command>
        </test>
        <test expect_num_outputs="3"> <!-- blat -->
            <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
            <param name="p" value="blastp"/>
            <expand macro="test_output_proteinortho" nlines="32"/>
            <expand macro="test_output_blastgraph" nlines="158"/>
            <expand macro="test_output_proteinorthograph" nlines="142"/>
            <assert_command>
                <has_text text="--p=blastp"/>
            </assert_command>
        </test>
    </tests>

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 once.
  | 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 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. 

----

**Proteinortho in a nutshell**

More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho

**Citations:**

- 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) 
- 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)

]]>
    </help>
    <expand macro="citations" /> <!--- TODO: citations are not working in usegalxy, therefore they are added manually at the above. -->
</tool>

7:c5dd4f86d981

<tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>detects orthologous proteins/genes within different species</description>
    <macros>
        <import>proteinortho_macros.xml</import>
        <xml name="test_output_proteinortho" tokens="nlines" token_nlines_delta="0">
            <output name="proteinortho">
                <metadata name="column_names" value="species,genes,alg.-conn.,L.fasta,C.fasta,E.fasta,M.fasta"/>
                <assert_contents>
                    <has_n_columns n="7"/>
                    <has_n_lines n="@NLINES@" delta="@NLINES_DELTA@"/>
                    <has_line_matching expression="# Species\tGenes\tAlg\.-Conn\.\t.*"/>
                    <has_line_matching expression="[0-9]+\t[0-9]+\t.*"/>
                    <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+.*"/>
                </assert_contents>
            </output>
        </xml>
        <xml name="test_output_blastgraph" tokens="nlines" token_nlines_delta="0">
            <output name="blastgraph">
                <metadata name="column_names" value="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba"/>
                <assert_contents>
                    <has_n_columns n="6" comment="#"/>
                    <has_n_lines n="@NLINES@" delta="@NLINES_DELTA@"/>
                    <has_line_matching expression="# file_a\tfile_b"/>
                    <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba"/>
                    <has_line_matching expression="# (C|C2|E|L|M)\.fasta\t(C|C2|E|L|M)\.fasta"/>
                    <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\t(C|C2|E|L|M)_[0-9]+.*"/>
                </assert_contents>

                #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 $more_options.selfblast:
            &&
            mv result.blast-graph_clean result.blast-graph;
        #end if
        #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 ;

    </outputs>
    <tests>
        <test expect_num_outputs="3"> <!-- test normal -->
            <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
            <param name="p" value="diamond"/>
            <expand macro="test_output_proteinortho" nlines="33" nlines_delta="5"/>
            <expand macro="test_output_blastgraph" nlines="156" nlines_delta="20"/>
            <expand macro="test_output_proteinorthograph" nlines="139" nlines_delta="20"/>
            <assert_command>
                <has_text text="--p=diamond"/>
            </assert_command>
        </test>
        <test expect_num_outputs="3"> <!-- various parameter -->

            <param name="conn" value="1"/>
            <param name="sim" value="42"/>
            <section name="more_options">
                <param name="cov" value="42"/>
                <param name="identity" value="42"/>
                <param name="singles" value="true"/>
                <param name="core" value="true"/>
            </section>
            <expand macro="test_output_proteinortho" nlines="151" nlines_delta="50"/>
            <expand macro="test_output_blastgraph" nlines="1403" nlines_delta="300"/>
            <expand macro="test_output_proteinorthograph" nlines="239" nlines_delta="150"/>
            <assert_command>
                <has_text text="--p=diamond"/>
            </assert_command>
        </test>
        <test expect_num_outputs="3"> <!-- synteny -->

            <param name="input_files_syn" value="L.gff,C.gff,E.gff,M.gff"/>
            <param name="p" value="diamond"/>
            <conditional name="synteny">
                <param name="synteny_options" value="specified"/>
            </conditional>
            <expand macro="test_output_proteinortho" nlines="38" nlines_delta="20"/>
            <expand macro="test_output_blastgraph" nlines="300" nlines_delta="150"/>
            <expand macro="test_output_proteinorthograph" nlines="119" nlines_delta="10" ncolumns="8" add_columns=",same_strand,simscore"/>
            <assert_command>
                <has_text text="--p=diamond"/>
            </assert_command>
        </test>
        <test expect_num_outputs="3"> <!-- blast -->
            <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
            <param name="p" value="blastp"/>
            <expand macro="test_output_proteinortho" nlines="33" nlines_delta="20"/>
            <expand macro="test_output_blastgraph" nlines="155" nlines_delta="50"/>
            <expand macro="test_output_proteinorthograph" nlines="139" nlines_delta="50"/>
            <assert_command>
                <has_text text="--p=blastp"/>
            </assert_command>
        </test>
        <test expect_num_outputs="3"> <!-- auto blast -->
            <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
            <param name="p" value="autoblast"/>
            <expand macro="test_output_proteinortho" nlines="33" nlines_delta="20"/>
            <expand macro="test_output_blastgraph" nlines="157" nlines_delta="50"/>
            <expand macro="test_output_proteinorthograph" nlines="136" nlines_delta="50"/>
            <assert_command>
                <has_text text="--p=autoblast"/>
            </assert_command>
        </test>
        <test expect_num_outputs="3"> <!-- last -->
            <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
            <param name="p" value="lastp"/>
            <expand macro="test_output_proteinortho" nlines="34" nlines_delta="20"/>
            <expand macro="test_output_blastgraph" nlines="148" nlines_delta="50"/>
            <expand macro="test_output_proteinorthograph" nlines="134" nlines_delta="50"/>
            <assert_command>
                <has_text text="--p=lastp"/>
            </assert_command>
        </test>
        <test expect_num_outputs="3"> <!-- blat -->
            <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
            <param name="p" value="blastp"/>
            <expand macro="test_output_proteinortho" nlines="33" nlines_delta="20"/>
            <expand macro="test_output_blastgraph" nlines="156" nlines_delta="50"/>
            <expand macro="test_output_proteinorthograph" nlines="136" nlines_delta="50"/>
            <assert_command>
                <has_text text="--p=blastp"/>
            </assert_command>
        </test>
    </tests>

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 once.
  | Details can be found in (doi:10.1186/1471-2105-12-124 and doi:10.3389/fbinf.2023.1322477).
  | 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. 

----

**Proteinortho in a nutshell**

More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho

**Citations:**

]]>
    </help>
    <expand macro="citations" /> <!--- TODO: citations are not working in usegalxy, therefore they are added manually at the above. -->
</tool>