# HG changeset patch
# User greg
# Date 1490193532 14400
# Node ID 7363c4e9423cb2c82aa5bd5173d07e9ba4b92e41
# Parent  0f498f13f10979d2c8b55891ee0fe49aea1038a7
Uploaded

diff -r 0f498f13f109 -r 7363c4e9423c phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Wed Mar 22 10:38:45 2017 -0400
+++ b/phylogenomics_analysis.xml	Wed Mar 22 10:38:52 2017 -0400
@@ -1,41 +1,33 @@
 <tool id="plant_tribes_phylogenomics_analysis" name="PhylogenomicsAnalysis" version="0.6.0">
     <description>builds gene family multiple sequence alignments and their corresponding phylogenies</description>
-    <requirements>
-        <requirement type="package" version="0.6">plant_tribes_phylogenomics_analysis</requirement>
-    </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-        <!-- In case the return code has not been set propery check stderr too -->
-        <regex match="Error:" />
-        <regex match="Exception:" />
-    </stdio>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <command>
         <![CDATA[
-            #if str($options_type.options_type_selector) == 'advanced':
-                #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond
+            #set input_format = $input_format_cond.input_format
+            #set scaffold = $input_format_cond.scaffold
+            #set method = $input_format_cond.method
+            #set options_type_cond = $input_format_cond.options_type_cond
+            #set options_type= $options_type_cond.options_type
+
+            #if str($options_type) == 'advanced':
+                #set multiple_sequence_alignments_cond = $options_type_cond.multiple_sequence_alignments_cond
                 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
                 #if str($multiple_sequence_alignments) == 'yes':
-                    #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
+                    #set multiple_sequence_alignments_option_cond = $options_type_cond.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
                     #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
-                    #set generate_output_aln = True
-                #else:
-                    #set generate_output_aln = False
                 #end if
-                #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
-                    #set generate_output_tree = True
-                #else:
-                    #set generate_output_tree = False
-                #end if
-            #else:
-                #set generate_output_aln = False
-                #set generate_output_tree = False
+                #set phylogenomic_trees_cond = $options_type_cond.phylogenetic_trees_cond
+                #set phylogenetic_trees = $phylogenomic_trees_cond.phylogenetic_trees
+                #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond
+                #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
             #end if
 
             python $__tool_directory__/phylogenomics_analysis.py
             --num_threads \${GALAXY_SLOTS:-4}
-            #set input_format = $input_format_cond.input_format
             #if str($input_format) == 'ptortho':
                 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
             #else:
@@ -51,7 +43,7 @@
             --scaffold '$scaffold.fields.path'
             --method $method
 
-            #if str($options_type.options_type_selector) == 'advanced':
+            #if str($options_type) == 'advanced':
                 #if str($multiple_sequence_alignments) == 'yes':
                     --alignments_method $multiple_sequence_alignments_option
                     #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
@@ -60,8 +52,8 @@
                     #end if
                 #end if
 
-                #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
-                    #set tree_inference_cond = $options_type.phylogenetic_trees_cond.tree_inference_cond
+                #if str($phylogenetic_trees) == 'yes':
+                    #set tree_inference_cond = $options_type_cond.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':
@@ -74,20 +66,21 @@
                         #end if
                         --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
+                    --max_orthogroup_size $options_type_cond.phylogenetic_trees_cond.max_orthogroup_size
+                    --min_orthogroup_size $options_type_cond.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
-                        --trim_type $trim_type_cond.trim_type
-                        #if str($trim_type_cond.trim_type) == 'gap_trimming':
-                            --gap_trimming $trim_type_cond.gap_trimming
-                        #end if
+                #if str($remove_gappy_sequences) == 'yes':
+                    #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
+                    #set trim_type = $trim_type_cond.trim_type
+                    #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
+                    #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
+                    #if str($remove_sequences_with_gaps) == 'yes':
+                        --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
+                    #end if
+                    --trim_type $trim_type_cond.trim_type
+                    #if str($trim_type_cond.trim_type) == 'gap_trimming':
+                        --gap_trimming $trim_type_cond.gap_trimming
                     #end if
                 #end if
             #end if
@@ -100,12 +93,12 @@
                 --output_ptorthocs_dir '$output_ptorthocs.files_path'
             #end if
 
-            #if $generate_output_aln:
+            #if str($multiple_sequence_alignments) == 'yes'
                 --output_aln '$output_aln'
                 --output_aln_dir '$output_aln.files_path'
             #end if
 
-            #if $generate_output_tree:
+            #if str($phylogenetic_trees) == 'yes':
                 --output_tree '$output_tree'
                 --output_tree_dir '$output_tree.files_path'
             #end if
@@ -119,120 +112,30 @@
             </param>
             <when value="ptortho">
                 <param name="input_ptortho" format="ptortho" type="data" label="Precomputed orthologous gene family clusters" />
-            </when>
-            <when value="ptorthocs">
-                <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" />
-                <conditional name="multiple_codon_alignments_cond">
-                    <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
-                        <option value="no" selected="True">No</option>
-                        <option value="yes">Yes</option>
-                    </param>
-                    <when value="no" />
-                    <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>
+                <expand macro="param_scaffold" />
+                <expand macro="param_method" />
+                <conditional name="options_type_cond">
+                    <expand macro="param_options_type" />
+                    <when value="basic" />
+                    <when value="advanced">
+                        <expand macro="cond_multiple_sequence_alignments" />
+                        <expand macro="cond_phylogenomic_trees" />
+                        <expand macro="cond_remove_gappy_sequences" />
                     </when>
                 </conditional>
             </when>
-        </conditional>
-        <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>
-            <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 alignments 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 method for multiple sequence alignments" 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 execute" />
-                            </when>
-                        </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">
-                                <conditional name="rooting_order_file_cond">
-                                    <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select No for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
-                                        <option value="no" selected="true">No</option>
-                                        <option value="yes">Yes</option>
-                                    </param>
-                                    <when value="no" />
-                                    <when value="yes">
-                                        <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
-                                    </when>
-                                </conditional>
-                                <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="gap_trimming" selected="true">Nucleotide based </option>
-                                        <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</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 value="ptorthocs">
+                <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" />
+                <expand macro="param_scaffold" />
+                <expand macro="param_method" />
+                <conditional name="options_type_cond">
+                    <expand macro="param_options_type" />
+                    <when value="basic" />
+                    <when value="advanced">
+                        <expand macro="cond_multiple_sequence_alignments" />
+                        <expand macro="cond_phylogenomic_trees" />
+                        <expand macro="cond_remove_gappy_sequences" />
+                        <expand macro="cond_multiple_codon_alignments" />
                     </when>
                 </conditional>
             </when>
@@ -245,11 +148,11 @@
         <data name="output_ptorthocs" format="ptorthocs">
             <filter>input_format_cond['input_format'] == 'ptorthocs'</filter>
         </data>
-        <data name="output_aln" format="ptalign" label="Multiple alignments using method ${options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option']} on ${on_string}">
-            <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
+        <data name="output_aln" format="ptalign" label="Multiple alignments (method ${options_type_cond['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option']}) on ${on_string}">
+            <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
         </data>
         <data name="output_tree" format="pttree" label="Phylogenetic trees on ${on_string}">
-            <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
+            <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
         </data>
     </outputs>
     <tests>
@@ -295,41 +198,5 @@
   - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).
 
     </help>
-    <citations>
-        <citation type="bibtex">
-            @misc{None,
-            journal = {None},
-            author = {1. Wafula EK},
-            title = {Manuscript in preparation},
-            year = {None},
-            url = {https://github.com/dePamphilis/PlantTribes},}
-        </citation>
-        <citation type="bibtex">
-            @article{Mirarab2014,
-            journal = {Research in Computational Molecular Biology (RECOMB)},
-            author = {2. Mirarab S, Nguyen N, Warnow T},
-            title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
-            year = {2014},
-            pages = {177–191},
-            url = {https://github.com/smirarab/pasta},}
-        </citation>
-        <citation type="bibtex">
-            @article{Salvador2009,
-            journal = {Bioinformatics},
-            author = {3. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T},
-            title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
-            year = {2009},
-            url = {http://trimal.cgenomics.org},}
-        </citation>
-        <citation type="bibtex">
-            @article{Stamatakis2014,
-            journal = {Bioinformatics},
-            author = {4. Stamatakis A},
-            title = {RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies},
-            year = {2014},
-            url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html},}
-        </citation>
-        <citation type="doi">10.1371/journal.pone.0009490</citation>
-        <citation type="doi">10.1093/bioinformatics/btw412</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>