annotate icescreen.xml @ 2:f08181349fc4 draft

"planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit f826da6f47b642df169ab0747d6363326e944114"

<tool id="icescreen" name="ICEscreen" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
    <description>detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes.</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.4</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">icescreen</requirement>
        <requirement type="package" version="3.0">zip</requirement>
    </requirements>
    <version_command><![CDATA[
        icescreen --version
        ]]>
    </version_command>
    <command detect_errors="aggressive"><![CDATA[
        #set $gbname = 'galaxy_genbank'
        mkdir -p ./tmp_icescreen/source_genbank
        && ln -s '${genome}' ./tmp_icescreen/source_genbank/${gbname}.gb
        && icescreen
            --galaxy
            --gbdir ./tmp_icescreen/source_genbank
            --outdir ./tmp_icescreen
            --mode '${taxonomy.mode}'
            --jobs "\${GALAXY_SLOTS:-4}" > ./tmp_icescreen/ICEscreen_log.txt 2>&1

        && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_ME.summary > '${summary}'
        && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_SP_withMEIds.tsv > '${detected_sp}'
        && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_ME.tsv > '${detected_me}'

        #if "output_annotation_genbank" in $additional_output.optional_files:
            && mv ./tmp_icescreen/ICEscreen_results/results/${gbname}/visualization_files/${gbname}_icescreen.gb '${gbout}'
        #end if
        #if "output_annotation_gff" in $additional_output.optional_files:
            && mv ./tmp_icescreen/ICEscreen_results/results/${gbname}/visualization_files/${gbname}_icescreen.gff '${gffout}'
        #end if
        #if "output_annotation_embl" in $additional_output.optional_files:
            && mv ./tmp_icescreen/ICEscreen_results/results/${gbname}/visualization_files/${gbname}_icescreen.embl '${emblout}'
        #end if
        #if "output_log" in $additional_output.optional_files:
            && mv ./tmp_icescreen/ICEscreen_log.txt '${log}'
        #end if
        #if "output_zip_all_files" in $additional_output.optional_files:
            && cd ./tmp_icescreen/ICEscreen_results/results/${gbname} && zip --quiet -r - -- . > '${outzip}'
        #end if
        ]]>
    </command>
    <inputs>
        <param name="genome" type="data" format="genbank" label="Input genomes to analyze in Genbank format" help=""/>
        <section name="taxonomy" title="Taxonomy of the genomes to analyse" expanded="False">
            <param name="mode" type="select" label="Firmicutes is the defaut parameter" help="Streptomyces is EXPERIMENTAL and is NOT recommended.">
                <option value="firmicutes" selected="true">Firmicutes</option>
                <option value="streptomyces">Streptomyces</option>
            </param>
        </section>
        <section name="additional_output" title="Additional output files" expanded="False">
            <param name="optional_files" type="select" label="Make the following optional files available in the Galaxy history" multiple="true" optional="true" display="checkboxes" >
                <option value="output_annotation_genbank">Genome annotation in genbank format</option>
                <option value="output_annotation_gff">Genome annotation in gff format</option>
                <option value="output_annotation_embl">Genome annotation in embl format</option>
                <option value="output_zip_all_files">Zip of all final and intermediate results</option>
                <option value="output_log">ICEscreen log</option>
            </param>
        </section>
    </inputs>
    <outputs>
      <data format="tabular" name="detected_sp" label="${tool.name} on ${on_string}: Signature Proteins table" />
      <data format="tabular" name="detected_me" label="${tool.name} on ${on_string}: ICEs/IMEs table" />
      <data format="txt" name="summary" label="${tool.name} on ${on_string}: results summary" />
      <data format="genbank" name="gbout" label="${tool.name} on ${on_string}: annotated genbank" >
          <filter>additional_output['optional_files'] and "output_annotation_genbank" in additional_output['optional_files']</filter>
      </data>
      <data format="gff3" name="gffout" label="${tool.name} on ${on_string}: annotated GFF3" >
          <filter>additional_output['optional_files'] and "output_annotation_gff" in additional_output['optional_files']</filter>
      </data>
      <data format="embl" name="emblout" label="${tool.name} on ${on_string}: annotated EMBL" >
          <filter>additional_output['optional_files'] and "output_annotation_embl" in additional_output['optional_files']</filter>
      </data>
      <data format="zip" name="outzip" label="${tool.name} on ${on_string}: all results zipped">
          <filter>additional_output['optional_files'] and "output_zip_all_files" in additional_output['optional_files']</filter>
      </data>
      <data format="txt" name="log" label="${tool.name} on ${on_string}: log file" >
          <filter>additional_output['optional_files'] and "output_log" in additional_output['optional_files']</filter>
      </data>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
            <output name="summary" file="NC_004668_137848_164286_detected_ME.summary" ftype="txt" />
            <output name="detected_me" file="NC_004668_137848_164286_detected_ME.tsv" ftype="tabular" />
            <output name="detected_sp" >
                <assert_contents>
                    <has_text text="ICE IME Number" />
                    <has_text text="WP_002359295" />
                    <has_text text="VirB4" />
                    <has_n_columns n="47" />
                    <has_n_lines n="5" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
            <param name="optional_files" value="output_annotation_genbank" />
            <output name="gbout" file="NC_004668_137848_164286_icescreen.gb" ftype="genbank" />
        </test>
        <test expect_num_outputs="4">
            <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
            <param name="optional_files" value="output_annotation_gff" />
            <output name="gffout" file="NC_004668_137848_164286_icescreen.gff" ftype="gff3" />
        </test>
        <test expect_num_outputs="4">
            <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
            <param name="optional_files" value="output_annotation_embl" />
            <output name="emblout" file="NC_004668_137848_164286_icescreen.embl" ftype="embl" />
        </test>
        <test expect_num_outputs="4">
            <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
            <param name="optional_files" value="output_zip_all_files" />

            <output name="outzip" >
                <assert_contents>
                    <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE IME Number" /></has_archive_member>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
            <param name="optional_files" value="output_log" />
            <output name="log" >
                <assert_contents>
                    <has_text text="firmicutes" />
                    <has_text text="Building DAG of jobs" />
                    <has_text text="Complete log" />
                    <not_has_text text="Error" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
            <param name="mode" value="streptomyces" />
            <param name="optional_files" value="output_log" />
            <output name="log" >
                <assert_contents>
                    <has_text text="streptomyces" />
                    <not_has_text text="Error" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
            <param name="mode" value="firmicutes" />
            <param name="optional_files" value="output_zip_all_files,output_log" />
            <output name="log" >
                <assert_contents>
                    <has_text text="firmicutes" />
                    <not_has_text text="Error" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        .. class:: warningmark

        This tool requires *genbank* format.

-----

        **What it does**

        ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes. The full documentation is available at https://icescreen.migale.inrae.fr. The forge of the project is accessible at https://forgemia.inra.fr/ices_imes_analysis/icescreen.

        **Main features of ICEscreen**

        - Detection of signature proteins (SPs) of ICEs/IMEs by using blastP on a curated resource.	BlastP allows for an accurate assignment of hits to a given ICE/IME superfamily or family. The curated resource was derived from an analysis of over 120 ICEs and IMEs in Streptococcus genomes by the DINAMIC lab.
        - Detection of distant homologs of SPs by using HMM profiles of ICEs/IMEs protein families. The HMM profiles have been either imported from trusted resources or created and curated when needed.
        - Detection of the ICE/IME structures: ICEScreen groups together SPs that belong to the same ICE/IME structures to the best of its ability.
        - Delimitation of the elements at the gene or nucleotide level is not yet implemented and still needs manual curation.

        **Output files**

        There are 3 main output results files generated by ICEscreen:

        - Detected Signature Proteins table (`*_detected_SP_withMEIds.csv`): list of the signature proteins detected by the tool and their possible assignment to an ICE or IME element. It is a comma separated table of 48 columns with a one line header. Each line represents a signature protein detected by ICEscreen.
        - Detected ICEs/IMEs table (`*_detected_ME.tsv`): list of the ICEs and IMEs elements detected by the tool, including information about the signature proteins they contain. It is a tab separated table of 21 columns, the header is at line #3. Information in this file is similar to the output file _withICEIMEIds.csv (option -m) but centered around a list of ICE / IME structures instead of a list of SPs.
        - Results summary (`*_detected_ME.summary`): this file summarizes the main parameters and statistics regarding the ICE / IME structures and the SPs.

        Other optional and additional output files generated by ICEscreen:

        - Annotated Genbank, EMBL, and GFF3 files: tose files contains the annotations of the original Genbank file in addition to annotations added by ICEscreen such as ICEscreen signature proteins and mobile elements.
        - All results zipped file: You can download this file locally and unzip it to have the complete output folder generated by the tool, including intermediate processing files. See https://icescreen.migale.inrae.fr for details.
        - Log file (`*_detected_ME.log`): this file contains the detailed internal details used by ICEscreen to generate the results and logs of each step of the ICEscreen tool pipeline.

    ]]>

    </help>
    <citations>
        <citation type="bibtex">@UNPUBLISHED{Kim07aninterior-point,
            author = {Julie Lao and Thomas Lacroix and Gérard Guédon and Charles Coluzzi and Nathalie Leblond-Bourget and Hélène Chiapello},
            title = {"See our latest publication at https://icescreen.migale.inrae.fr."}
        }
        </citation>
    </citations>
</tool>