comparison goprofiles.xml @ 12:d4dd1c242a87 draft

planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72

11:3ddc1f78773d

<tool id="goProfiles" name="Statistical analysis of functional profiles" version="2019.06.27">
    <description>(Human, Mouse) [goProfiles]</description>
    <requirements> 
        <requirement type="package" version="3.4.1">R</requirement>
        <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
        <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
        <!--requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement-->
        <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
        <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
        <requirement type="package" version="1.38.0">goprofiles</requirement>
        
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[

            --input_type="file"
            --input="$input.file"
            --ncol="$input.ncol"
            --header="$input.header"
        #end if
        
        --id_type="$input.id_type"
        --onto_opt="$onto_opt"
        --plot_opt="$plot_opt"
        --level="$level"
        --per="$per"

                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
                <param name="id_type" type="select" label="Select type of IDs list" >
                    <option value="Entrez">Entrez Gene ID</option>
                    <option value="UniProt">Uniprot Accession number</option>
                </param>
            </when>            
        </conditional>
        <param name="duplicate" type="boolean" checked="true" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
        <param name="species" type="select" label="Species">
            <option value="org.Hs.eg.db">Human (Homo sapiens)</option>
            <option value="org.Mm.eg.db">Mouse (Mus musculus)</option>

                <valid initial="string.printable">
                    <remove value="&apos;"/>
                    <remove value="/"/>
                </valid>
                <mapping>
                    <add source="&#x20;" target=""/> 
                </mapping>
            </sanitizer>
        </param>
        <param type="select" name="plot_opt" label="Plot file format">
            <option value="PNG" selected="True">png</option>

        <test>
            <conditional name="input">
                <param name="ids" value="file" />
                <param name="file" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" />
                <param name="ncol" value="c1" />
                <param name="header" value="true" /> 
                <param name="id_type" value="UniProt" />              
            </conditional>
            <param name="duplicate" value="false"/>
            <param name="onto_opt" value="CC,MF,BP" />
            <param name="level" value="2" />
            <param name="per" value="true" />

    <help><![CDATA[

**Description**

This tool relies on the goProfiles R package; it performs statistical analysis of functional profiles based on Gene Ontology (GO). Functional profile at a given GO level is obtained by counting the
number of identifiers having a hit in each category of this level.   

-----

**Input** 

Two modes are allowed: either by copy/pasting your IDs (separated by a space) or by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers).
Only entrez gene ID (e.g. 4151) or Uniprot accession number (e.g. P31946) are allowed. If your list is not in this form, please use the ID_Converter tool of ProteoRE. 

.. class:: warningmark
	
In copy/paste mode, the number of IDs considered in input is limited to 5000.

-----

**Parameters**

"Species": enter the sepcies you are working on; Homo sapiens and Mus musculus supported (Rattus norvegicus coming soon)

"Select GO terms category": you can choose one or more GO categories which are Biological Process (BP), Cellular Component (CC) and Molecular Function (MF) 

"Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 6). In general the higher the level, the more semantically specific the term is.

-----

**Ouput**

Diagram output: graphical output in the form of bar-plot or dot-plot (png (default format), jpeg or pdf format), one figure for each GO category. 

Text output: with the following information GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) and GO term frequency (e.g. BP.Frequency)

-----

.. class:: infomark

Packages used: 
    - bioconductor-org.hs.eg.db v3.5.0
    - bioconductor-org.mm.eg.db v3.5.0
    - bioconductor-annotationdbi v1.40.0
    - bioconductor-biobase v2.98.0
    - goprofiles v1.38.0

-----

.. class:: infomark

**Authors** 

Salicrú M, Ocaña J, Sánchez-Pla A. Comparison of lists of genes based on functional profiles. BMC Bioinformatics. 2011. 12:401. doi:10.1186/1471-2105-12-401. PubMed PMID: 21999355

-----

12:d4dd1c242a87

<tool id="goProfiles" name="Statistical analysis of functional profiles" version="2019.09.26">
    <description>(Human, Mouse) [goProfiles]</description>
    <requirements>
        <requirement type="package" >R</requirement>
        <requirement type="package" version="3.8.2">-org.hs.eg.db</requirement>
        <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement>
        <!--requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement-->
        <requirement type="package" version="1.46.0">bioconductor-annotationdbi</requirement>
        <requirement type="package" version="2.44.0">bioconductor-biobase</requirement>
        <requirement type="package" version="1.46.0">bioconductor-goprofiles</requirement>

    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[

            --input_type="file"
            --input="$input.file"
            --ncol="$input.ncol"
            --header="$input.header"
        #end if

        --id_type="$input.id_type"
        --onto_opt="$onto_opt"
        --plot_opt="$plot_opt"
        --level="$level"
        --per="$per"

                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
                <param name="id_type" type="select" label="Select type of IDs list" >
                    <option value="Entrez">Entrez Gene ID</option>
                    <option value="UniProt">Uniprot Accession number</option>
                </param>
            </when>
        </conditional>
        <param name="duplicate" type="boolean" checked="true" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
        <param name="species" type="select" label="Species">
            <option value="org.Hs.eg.db">Human (Homo sapiens)</option>
            <option value="org.Mm.eg.db">Mouse (Mus musculus)</option>

                <valid initial="string.printable">
                    <remove value="&apos;"/>
                    <remove value="/"/>
                </valid>
                <mapping>
                    <add source="&#x20;" target=""/>
                </mapping>
            </sanitizer>
        </param>
        <param type="select" name="plot_opt" label="Plot file format">
            <option value="PNG" selected="True">png</option>

        <test>
            <conditional name="input">
                <param name="ids" value="file" />
                <param name="file" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" />
                <param name="ncol" value="c1" />
                <param name="header" value="true" />
                <param name="id_type" value="UniProt" />
            </conditional>
            <param name="duplicate" value="false"/>
            <param name="onto_opt" value="CC,MF,BP" />
            <param name="level" value="2" />
            <param name="per" value="true" />

    <help><![CDATA[

**Description**

This tool relies on the goProfiles R package; it performs statistical analysis of functional profiles based on Gene Ontology (GO). Functional profile at a given GO level is obtained by counting the
number of identifiers having a hit in each category of this level.

-----

**Input**

Two modes are allowed: either by copy/pasting your IDs (separated by a space) or by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers).
Only entrez gene ID (e.g. 4151) or Uniprot accession number (e.g. P31946) are allowed. If your list is not in this form, please use the ID_Converter tool of ProteoRE.

.. class:: warningmark

In copy/paste mode, the number of IDs considered in input is limited to 5000.

-----

**Parameters**

"Species": enter the sepcies you are working on; Homo sapiens and Mus musculus supported (Rattus norvegicus coming soon)

"Select GO terms category": you can choose one or more GO categories which are Biological Process (BP), Cellular Component (CC) and Molecular Function (MF)

"Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 6). In general the higher the level, the more semantically specific the term is.

-----

**Ouput**

Diagram output: graphical output in the form of bar-plot or dot-plot (png (default format), jpeg or pdf format), one figure for each GO category.

Text output: with the following information GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) and GO term frequency (e.g. BP.Frequency)

-----

.. class:: infomark

Packages used:
    - bioconductor-org.hs.eg.db v3.5.0
    - bioconductor-org.mm.eg.db v3.5.0
    - bioconductor-annotationdbi v1.40.0
    - bioconductor-biobase v2.98.0
    - goprofiles v1.38.0

-----

.. class:: infomark

**Authors**

Salicrú M, Ocaña J, Sánchez-Pla A. Comparison of lists of genes based on functional profiles. BMC Bioinformatics. 2011. 12:401. doi:10.1186/1471-2105-12-401. PubMed PMID: 21999355

-----