diff phylogenomics_analysis.xml @ 0:30c4554064f9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogenomics_analysis.xml	Sat Dec 24 10:42:48 2016 -0500
@@ -0,0 +1,218 @@
+<tool id="plant_tribes_phylogenomics_analysis" name="PhylogenomicsAnalysis" version="1.0.0">
+    <description>pipeline</description>
+    <requirements>
+        <requirement type="package" version="0.2">plant_tribes_phylogenomics_analysis</requirement>
+    </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <!-- In case the return code has not been set properly check stderr too -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+    <command>
+        <![CDATA[
+            PhylogenomicsAnalysis
+            ----orthogroup_faa "$orthogroup_fna.extra_files_path"
+            --scaffold "$scaffold"
+            --method $method
+            #if str($options_type.options_type_selector) == 'advanced':
+                #if str($options_type.multiple_sequence_alignments_cond) == 'yes':
+                    #set multiple_codon_alignments_cond = $options_type.multiple_sequence_alignments_cond.multiple_codon_alignments_cond
+                    #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
+                    #if str($multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'create_alignments':
+                        --create_alignments
+                    #else if str($multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'add_alignments':
+                        --add_alignments
+                    #else if str($multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'pasta_alignments':
+                        --pasta_alignments
+                        --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
+                    #end if
+                    #if str($multiple_codon_alignments_cond.multiple_codon_alignments) == 'yes':
+                        --codon_alignments
+                        --orthogroup_fna "$orthogroup_fna"
+                        --sequence_type $multiple_codon_alignments_cond.sequence_type
+                    #end if
+                #end if
+                #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
+                    #set tree_inference_cond = $options_type.phylogenetic_trees_cond.tree_inference_cond
+                    #set tree_inference_method = $tree_inference_cond.tree_inference
+                    --tree_inference $tree_inference_method
+                    #if str($tree_inference_method) == 'raxml':
+                        --rooting_order "$tree_inference_cond.rooting_order"
+                        --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
+                    #end if
+                    --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size
+                    --min_orthogroup_size $options_type.phylogenetic_trees_cond.min_orthogroup_size
+                #end if
+                #if str($options_type.msa_quality_control_options_cond.msa_quality_control_options) == 'yes':
+                    #set msa_quality_control_options_cond = $options_type.msa_quality_control_options_cond
+                    #set remove_gappy_sequences_cond = $msa_quality_control_options_cond.remove_gappy_sequences_cond
+                    #if str($remove_gappy_sequences_cond) == 'yes':
+                        #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
+                        --remove_sequences $remove_gappy_sequences_cond.remove_sequences
+                        #if str($trim_type_cond.trim_type) == 'automated_trimming':
+                            --automated_trimming
+                        else:
+                            --gap_trimming $trim_type_cond.gap_trimming
+                        #end if
+                    #end if
+                #end if
+            #end if
+            --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
+            --num_threads \${GALAXY_SLOTS:-4}
+        ]]>
+    </command>
+    <inputs>
+        <param name="orthogroup_fna" format="fasta" type="data" label="Gene family classification coding sequences (CDS) fasta file for which orthogroup fasta files were created"/>
+        <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 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>
+            <option value="orthofinder">OrthoFinder</option>
+            <option value="orthomcl">OrthoMCL</option>
+        </param>
+        <conditional name="options_type">
+            <param name="options_type_selector" type="select" label="Options Configuration">
+                <option value="basic" selected="true">Basic</option>
+                <option value="advanced">Advanced</option>
+            </param>
+            <when value="basic" />
+            <when value="advanced">
+                <conditional name="multiple_sequence_alignments_cond">
+                    <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignemnts options?">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <conditional name="multiple_sequence_alignments_option_cond">
+                            <param name="multiple_sequence_alignments_option" label="Select option" type="select" force_select="True">
+                                <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
+                                <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
+                                <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
+                            </param>
+                            <when value="create_alignments"/>
+                            <when value="add_alignments"/>
+                            <when value="pasta_alignments">
+                                <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iteration that the PASTA algorithm will run"/>
+                            </when>
+                        </conditional>
+                        <conditional name="multiple_codon_alignments_cond">
+                            <param name="multiple_codon_alignments" label="Construct orthogroup multiple codon alignments?" type="select">
+                                <option value="no" selected="True">No</option>
+                                <option value="yes">Yes</option>
+                            </param>
+                            <when value="yes">
+                                <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference - (dna)">
+                                    <option value="protein" selected="true">Amino acid based</option>
+                                    <option value="dna">Nucleotide based</option>
+                                </param>
+                            </when>
+                            <when value="no"/>
+                        </conditional>
+                    </when>
+                </conditional>
+                <conditional name="phylogenetic_trees_cond">
+                    <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <conditional name="tree_inference_cond">
+                            <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
+                                <option value="raxml" selected="true">RAxML</option>
+                                <option value="fasttree">FastTree</option>
+                            </param>
+                            <when value="raxml">
+                                <param name="rooting_order" format="txt" type="data" label="Select file containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees"/>
+                                <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree"/>
+                            </when>
+                            <when value="fasttree"/>
+                        </conditional>
+                        <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments"/>
+                        <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments"/>
+                    </when>
+                </conditional>
+                <conditional name="msa_quality_control_options_cond">
+                    <param name="msa_quality_control_options" type="select" label="Set MSA quality control options?">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <conditional name="remove_gappy_sequences_cond">
+                            <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
+                                <option value="no" selected="true">No</option>
+                                <option value="yes">Yes</option>
+                            </param>
+                            <when value="no"/>
+                            <when value="yes">
+                                <param name="remove_sequences" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps"/>
+                                <conditional name="trim_type_cond">
+                                    <param name="trim_type" type="select" label="Select process used for gap trimming">
+                                        <option value="automated_trimming" selected="true">Trim alignments using trimAl's ML heuristic trimming approach</option>
+                                        <option value="gap_trimming">Nucleotide based</option>
+                                    </param>
+                                    <when value="automated_trimming"/>
+                                    <when value="gap_trimming">
+                                        <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps"/>
+                                    </when>
+                                </conditional>
+                            </when>
+                        </conditional>
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <collection name="transcripts" type="list">
+            <discover_datasets pattern="__name__" directory="phylogenomicsAnalysis_dir" visible="true" ext="fasta" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="" ftype="fasta" />
+            <param name="prediction_method" value="transdecoder"/>
+            <param name="target_gene_family_assembly" value="no"/>
+            <param name="strand_specific" value="yes"/>
+            <param name="dereplicate" value="yes"/>
+            <param name="min_length" value="200"/>
+            <output_collection name="orthos" type="list">
+
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
+complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
+analyses, comparing and analyzing the sequences of single genes, or a small number of genes, as well as many other types of data.
+
+-----
+
+**Options**
+
+ * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
+ * **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL.
+ * **Protein classification method** - One of blastp, HMMScan or both.
+ * **SuperOrthogroups MCL clustering** - blastp e-value matrix between all pairs of orthogroups.
+ * **Minumum single copy taxa required in orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
+ * **Minumum taxa required in single copy orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
+ * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?".
+ 
+    </help>
+    <citations>
+            <citation type="bibtex">
+                @unpublished{None,
+                author = {None},
+                title = {None},
+                year = {None},
+                eprint = {None},
+                url = {None}
+            }</citation>
+    </citations>
+</tool>