<tool id="kegg_pathways_visualization" name="KEGG pathways" version="2018.11.08">
    <description>map visualisation (PathView)</description>
    <requirements>
        <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript $__tool_directory__/kegg_pathways_visualization.R 
        #if $input.ids == "text"
            --id_list="$input.txt"
        #else
            --input="$input.file"
            --id_column="$input.ncol"
            --header="$input.header"  
        #end if
        #if $species.pathways.pathways_id != "pathways_file"
            --pathways_id="$species.pathways.pids" 
        #else 
            --pathways_input="$species.pathways.file"
            --header2="$species.pathways.header2"
            --pathway_col="$species.pathways.ncol2"
        #end if
        --id_type="$id_type"  
        --native_kegg="$native"
        

        #if $input.ids=="file" and $input.foldchange.fc=="true"
            --fold_change_data="$input.foldchange.fc"
            --fold_change_col="$input.foldchange.fc_col"
        #else 
            --fold_change_data="false"
        #end if

        --species=${species.ref_file} 
        --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] } 
        --output="$text_output"

    ]]></command>
    <inputs>
        <conditional name="species">
        <param name="ref_file" type="select" label="Select species" >
            <option value="hsa">Human (H. sapiens)</option>
            <option value="mmu">Mouse (M. musculus)</option>
            <option value="rno">Rat (R. norvegicus)</option>
        </param>
            <when value="hsa">
                <conditional name="pathways">
                <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
                    <option value="pathways_names">KEGG pathway name(s)</option>
                    <option value="pathways_ids">KEGG pathway id(s)</option>
                    <option value="pathways_file">KEGG pathway id(s) from file</option>
                </param>
                <when value="pathways_names">
                    <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
                        <options from_data_table="hsa_pathways">
                            <filter type="sort_by" column="1"/>
                            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                        </options>
                    </param>
                </when>
                <when value="pathways_ids">
                    <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'>
                        <sanitizer invalid_char=''>
                        <valid initial="string.printable">
                            <remove value="&apos;"/>
                        </valid>
                        <mapping>
                            <add source="&#x20;" target=""/> 
                        </mapping>
                        </sanitizer>
                    </param>
                </when>
                <when value="pathways_file">
                    <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
                    <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
                    <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
                </when>
                </conditional>
            </when>
            <when value="mmu">
                <conditional name="pathways">
                <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
                    <option value="pathways_names">KEGG pathway name(s)</option>
                    <option value="pathways_ids">KEGG pathway id(s)</option>
                    <option value="pathways_file">KEGG pathway id(s) from file</option>
                </param>
                <when value="pathways_names">
                    <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
                        <options from_data_table="mmu_pathways">
                            <filter type="sort_by" column="1"/>
                            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                        </options>
                    </param>
                </when>
                <when value="pathways_ids">
                    <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by tab, space or carriage return into the form field, for example: "mmu00053 mmu00340"'>
                        <sanitizer invalid_char=''>
                        <valid initial="string.printable">
                            <remove value="&apos;"/>
                        </valid>
                        <mapping>
                            <add source="&#x20;" target=""/> 
                        </mapping>
                        </sanitizer>
                    </param>
                </when>
                <when value="pathways_file">
                    <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id " help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" />
                    <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
                    <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
                </when>
                </conditional>
            </when>
            <when value="rno">
                <conditional name="pathways">
                <param name="pathways_id" type="select" label="Enter your pathway(s) name/id" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
                    <option value="pathways_names">KEGG pathway name(s)</option>
                    <option value="pathways_ids">KEGG pathway id(s)</option>
                    <option value="pathways_file">KEGG pathway id(s) from file</option>
                </param>
                <when value="pathways_names">
                    <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
                        <options from_data_table="rno_pathways">
                            <filter type="sort_by" column="1"/>
                            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                        </options>
                    </param>
                </when>
                <when value="pathways_ids">
                    <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'>
                        <sanitizer invalid_char=''>
                        <valid initial="string.printable">
                            <remove value="&apos;"/>
                        </valid>
                        <mapping>
                            <add source="&#x20;" target=""/> 
                        </mapping>
                        </sanitizer>
                    </param>
                </when>
                <when value="pathways_file">
                    <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
                    <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
                    <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
                </when>
                </conditional>
            </when>
        </conditional>
        <param name="id_type" type="select" label="Select your identifiers type :">
            <option value="uniprotID">Uniprot Accession number</option>
            <option value="geneID">Entrez gene ID</option>
            <!--option value="keggid">KEGG genes ID</option-->
        </param>
        <conditional name="input" >
            <param name="ids" type="select" label="Enter your identifiers (Uniprot AC or Entrez gene ID)" help="Copy/paste or ID list from a file (e.g. table)" >
                <option value="text">Copy/paste your identifiers</option>
                <option value="file" selected="true">Input file containing your identifiers</option>
            </param>
            <when value="text" >
                <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by tab, space or carriage return into the form field, for example: P31946 P62258' >
                    <sanitizer invalid_char=''>
                        <valid initial="string.printable">
                            <remove value="&apos;"/>
                        </valid>
                        <mapping initial="none">
                            <add source="&apos;" target="__sq__"/>
                        </mapping>
                    </sanitizer>
                </param>
            </when>
            <when value="file" >
                <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" />
                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
                <param name="ncol" type="text" value="c1" label="The column which contains your IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
                <conditional name="foldchange" >
                <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Do you have fold change values to represent on the graph ?" default="false"/>
                    <when value="true">
                        <param name="fc_col" type="text" label="Please enter column(s) number of fold change data separated by ','. 3 columns max" help="For example : c1,c3,c4"/>
                    </when>
                    <when value="false"/>
                </conditional>
            </when>
        </conditional>
        <param name="native" type="select" label="Choose the output graphical format">
            <option value="true">KEGG map (.png)</option>
            <option value="false">Graphviz layout engine (.pdf)</option> 
        </param>
    </inputs>
    <outputs>
        <data name="text_output" format="tsv" label="KEGG pathways visualization text output"/>
        <collection type="list" label="KEGG pathways map from ${input.file.name}" name="graphviz_output_from_file">
            <filter>native=="false" and input["ids"] == "file"</filter>
                <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.pdf" ext="pdf" />
        </collection>
        <collection type="list" label="KEGG pathways map from ${input.file.name}" name="kegg_graph_output_from_file">
            <filter>native=="true" and input["ids"] == "file"</filter>
                <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png"/>
        </collection>
        <collection type="list" label="KEGG pathways map" name="graphviz_output_from_list">
            <filter>native=="false" and input["ids"] == "text"</filter>
                <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.pdf" ext="pdf" />
        </collection>
        <collection type="list" label="KEGG pathways map" name="kegg_graph_output_from_list">
            <filter>native=="true" and input["ids"] == "text"</filter>
                <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png" />
        </collection>
    </outputs>
    <tests>
        <test>
            <conditional name="input">
                <param name="ids" value="file"/>
                <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
                <param name="header" value="true"/>
                <param name="ncol" value="c1"/>
            </conditional>
            <conditional name="pathways">
                <param name="pathways_id" value="pathways_ids"/>
                <param name="pids" value="04514,05167,00010"/>
            </conditional>
            <param name="id_type" value="uniprotID"/>
            <param name="species" value="hsa"/>
            <param name="native" value="true"/>            
            <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/>
            <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/>
            <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package.

You can map Entrez gene IDs / Uniprot accession number from three species : human, mouse and rat.

If your input have another type of IDs, please use the ID_Converter tool.

**Input:**


- KEGG Pathways IDs to be used for mapping can be set by:
    - chosing from the KEGG pathways name list 
    - giving a list (copy/paste)
    - importing a list from a dataset (column) - output of KEGG pathways identification and coverage can be used (1st column)
- Genes/proteins ids to map can be either a list of Entrez genes IDs / Uniprot accession number or a file (tabular, tsv, txt) containing at least one column of Entrez genes IDs / Uniprot accession number. 
- fold change values (up to three columns) from a dataset (same dataset as for Genes/proteins ids to map)

You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values.

.. csv-table:: Simulated data
   :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"

   "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759"
   "P02538","Keratin, type II cytoskeletal 6A","53","-0.988842456122076","0.654626325100182","-0.219153396366064"
   "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729"
   "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788"

|

**Output:**

- a **collection dataset** named 'KEGG pathways map from <dataset>', one file (png or pdf) for each given pathway.
- a **summary text file** (.tsv) of the mapping(s) with the following columns
    - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
    - **pathway name**: name(s) of KEGG pathway(s) used for mapping
    - **nb of Uniprot_AC used** (only when Uniprot accession number is given): number of Uniprot accession number which will be converted to Entrez genes IDs
    - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping
    - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway
    - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway
    - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs
    - **Entrez gene ID mapped**: list of mapped Entrez gene IDs
    - **uniprot_AC mapped** (only when Uniprot accession number is given): list of Uniprot accession number corresponding to the mapped Entrez gene IDs

-----

.. class:: infomark

**Database:**

KEGG Pathways names list are from  http://rest.kegg.jp/list/pathway/

User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html


-----

.. class:: infomark

**Authors**

David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR

Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform

This work has been partially funded through the French National Agency for Research (ANR) IFB project.

Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gkx372</citation>
        <citation type="bibtex">
@misc{renameTODO,
  author = {Weijun Luo},
  year = {2013},
  title = {pathview},
  url = {https://bioconductor.org/packages/release/bioc/html/pathview.html},
}</citation>
    </citations>
</tool>