comparison assembly_post_processor.xml @ 33:0a292e319d0c draft

Uploaded

32:9987e210180a

                        <option value="yes">Yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param name="orthogroups" format="tabular" type="data" label="Targeted gene families"/>
                        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
                            <options from_data_table="plant_tribes_scaffolds" />
                            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
                        </param>
                        <param name="method" type="select" label="Protein clustering method">
                            <option value="gfam" selected="true">GFam</option>

                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
            </output_collection>
        </test>
    </tests>
    <help>
This tool is one of the PlantTribes' collection of automated modular analysis pipelines for comparative and
evolutionary analyses of genome-scale gene families and transcriptomes.  This tool post-processes de novo
assembled transcripts into putative coding sequences and their corresponding amino acid translations and
optionally assigns transcripts to circumscribed gene families ("orthogroups")[2].  After transcripts have been
assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the
de novo assembly.  

-----

**Required options**

 * **Transcriptome assembly fasta file** - either de novo or reference-guided transcriptome assembly fasta file selected from your history.
 * **Coding regions prediction method** - method for finding coding recions within transcripts.  Available methods are TransDecoder[3] and ESTScan[4].
 * **Scores matrices** - scores matrices, based on a related species, are required when ESTScan is ued to find coding regions.  Details of how to create species-specific scores matrices can be found on the ESTScan website (http://estscan.sourceforge.net).  Matrices of some organisms are also available to download.

**Other options**

 * **Perform targeted gene assembly?** - selecting 'Yes' enables local assembly of one or more targeted gene families in a specific scaffold.  Scaffolds are defined in PlantTribes as clusters of paralogous/orthologous sequences from a specified set of proteomes[5-7].
 * **Targeted gene families** - select a history item containing a list of targeted orthogroup identifiers corresponding to the gene family classification from a specified scaffold.  Gene identifiers can be obtained from the function annotation table ("Orthogroup ID" field of .summary file) of scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool.
 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds (installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool) whose orthogroups(s) are targeted for the localized assembly.
 * **Protein clustering method** - gene family scaffold protein clustering method.  Each PlantTribes scaffold data has up to three sets of clusters - GFam[8] (clusters of consensus domain architecture), OrthoFinder[9] (broadly defined clusters) or OrthoMCL[10] (narrowly defined clusters).  You can also install your own data scaffold created using a different clustering method as long as it conforms to the PlantTribes scaffold data format.
 * **Trim alignments** - trim gene family multiple sequence alignments that include scaffold backbone genes and locally assembled transcripts to remove non-conserved regions (gappy sites)[11].  The trimmed alignments are used in assigning scores to locally assembled transcripts to determine how well they compare to the backbones gene models.  The default setting of 0.1 removes sites tha thave gaps in 90% of the sequences in the multiple sequence alignment.  This option is restricted to the range 0.0 - 1.0.
 * **Strand-specific assembly?** - select 'Yes' if transcriptome library sequences were strand-specific.  If 'Yes" is selected, transcripts from the minority strand (antisense) are removed.
 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp.

    </help>

33:0a292e319d0c

                        <option value="yes">Yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param name="orthogroups" format="tabular" type="data" label="Targeted gene families"/>
                        <param name="scaffold" type="select" label="Gene family scaffold">
                            <options from_data_table="plant_tribes_scaffolds" />
                            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
                        </param>
                        <param name="method" type="select" label="Protein clustering method">
                            <option value="gfam" selected="true">GFam</option>

                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
            </output_collection>
        </test>
    </tests>
    <help>
This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and
evolutionary analyses of genome-scale gene families and transcriptomes.  This tool post-processes de novo
assembled transcripts into putative coding sequences and their corresponding amino acid translations and
optionally assigns transcripts to circumscribed gene families ("orthogroups")[2].  After transcripts have been
assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the
de novo assembly.  

-----

**Required options**

 * **Transcriptome assembly fasta file** - either de novo or reference-guided transcriptome assembly fasta file selected from your history.
 * **Coding regions prediction method** - method for finding coding regions within transcripts.  Available methods are TransDecoder[3] and ESTScan[4].
 * **Scores matrices** - scores matrices, based on a related species, are required when ESTScan is used to find coding regions.  Details of how to create species-specific scores matrices can be found on the ESTScan website (http://estscan.sourceforge.net).  Matrices of some organisms are also available to download.

**Other options**

 * **Perform targeted gene assembly?** - selecting 'Yes' enables local assembly of one or more targeted gene families in a specific scaffold.  Scaffolds are defined in PlantTribes as clusters of paralogous/orthologous sequences from a specified set of proteomes[5-7].
 * **Targeted gene families** - select a history item containing a list of targeted orthogroup identifiers corresponding to the gene family classification from a specified scaffold.  Gene identifiers can be obtained from the function annotation table ("Orthogroup ID" field of .summary file) of scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and also available at the PlantTribes github repository (https://github.com/dePamphilis/PlantTribes/tree/master/config).
 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds (installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool) whose orthogroups(s) are targeted for the localized assembly.
 * **Protein clustering method** - gene family scaffold protein clustering method.  Each PlantTribes scaffold data has up to three sets of clusters - GFam[8] (clusters of consensus domain architecture), OrthoFinder[9] (broadly defined clusters) or OrthoMCL[10] (narrowly defined clusters).  You can also install your own data scaffold created using a different clustering method as long as it conforms to the PlantTribes scaffold data format.
 * **Trim alignments** - trim gene family multiple sequence alignments that include scaffold backbone genes and locally assembled transcripts to remove non-conserved regions (gappy sites)[11].  The trimmed alignments are used in assigning scores to locally assembled transcripts to determine how well they compare to the backbone gene models.  The default setting of 0.1 removes sites that have gaps in 90% of the sequences in the multiple sequence alignment.  This option is restricted to the range 0.0 - 1.0.
 * **Strand-specific assembly?** - select 'Yes' if transcriptome library sequences were strand-specific.  If 'Yes" is selected, transcripts from the minority strand (antisense) are removed.
 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp.

    </help>