# HG changeset patch
# User greg
# Date 1486486098 18000
# Node ID 46f43a90492a60c62f5e91aa9398c63c0118cba7
# Parent  8d1dbff426598a04f977e66c0c6ae06160c9a6d3
Uploaded

diff -r 8d1dbff42659 -r 46f43a90492a gene_family_classifier.xml
--- a/gene_family_classifier.xml	Mon Feb 06 11:32:27 2017 -0500
+++ b/gene_family_classifier.xml	Tue Feb 07 11:48:18 2017 -0500
@@ -21,23 +21,40 @@
             #if str($options_type.options_type_selector) == 'advanced':
                 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
                 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
+                #set specify_single_copy_cond = $options_type.specify_single_copy_cond
+                #set specify_single_copy = $specify_single_copy_cond.single_copy_cond
+
+                #if str($specify_single_copy) == 'yes':
+                    #set specify_single_copy = True
+                    #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
+                    #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
+                    #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
+                    ## FixMe: the single_copy_custom option is not currently supported.
+                    #set single_copy = $single_copy_cond.single_copy
+
+                    mkdir -p $single_copy_fasta_dest_dir &&
+                #else:
+                    #set specify_single_copy = False
+                #end if
 
                 #if str($create_orthogroup) == 'yes':
+                    #set create_ortho_sequences = True
+                    #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
                     #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
+
                     #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
                         #set create_corresponding_coding_sequences = True
                     #else:
                         #set create_corresponding_coding_sequences = False
                     #end if
 
-                    #set create_ortho_sequences = True
-                    #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
                     #if $create_corresponding_coding_sequences:
-                        #set dest_dir = $output_ptcgfcs.extra_files_path
+                        #set orthogroups_fasta_dest_dir = $output_ptcgfcs.extra_files_path
                     #else:
-                        #set dest_dir = $output_ptcgf.extra_files_path
-                      #end if
-                    mkdir -p $dest_dir &&
+                        #set orthogroups_fasta_dest_dir = $output_ptcgf.extra_files_path
+                    #end if
+
+                    mkdir -p $orthogroups_fasta_dest_dir &&
                 #else:
                     #set create_ortho_sequences = False
                     #set create_corresponding_coding_sequences = False
@@ -57,9 +74,9 @@
 
             #if str($options_type.options_type_selector) == 'advanced':
                 --super_orthogroups $options_type.super_orthogroups
-                #if str($options_type.single_copy_cond) == 'taxa':
-                    --single_copy_taxa $options_type.single_copy_cond.single_copy_taxa
-                    --taxa_present $options_type.single_copy_cond.taxa_present
+                #if $specify_single_copy:
+                    --single_copy_taxa $single_copy_cond.single_copy_taxa
+                    --taxa_present $single_copy_cond.taxa_present
                 #end if
                 #if str($create_orthogroup) == 'yes':
                     --orthogroup_fasta
@@ -68,6 +85,7 @@
                     #end if
                 #end if
             #end if
+            >/dev/null
 
             #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both':
                 #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
@@ -79,17 +97,17 @@
 
             #if $create_ortho_sequences:
                 #if $create_corresponding_coding_sequences:
-                    && echo "#Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptcgfcs
-                    && echo -e "#Size\t\tFile" >> $output_ptcgfcs
-                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t\t"$9}' >> $output_ptcgfcs
+                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptcgfcs
                 #else:
-                    && echo "#Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptcgf
-                    && echo -e "#Size\t\tFile" >> $output_ptcgf
-                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t\t"$9}' >> $output_ptcgf
+                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptcgf
                 #end if
-                && mv $orthogroups_fasta_src_dir/* $dest_dir || true
+                && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true
             #end if
 
+            #if $specify_single_copy:
+                && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptsco
+                && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true
+            #end if
         ]]>
     </command>
     <inputs>
@@ -134,15 +152,30 @@
                     <option value="min_evalue" selected="true">Minimum e-value</option>
                     <option value="avg_evalue">Average e-value</option>
                 </param>
-                <conditional name="single_copy_cond">
-                    <param name="single_copy" type="select" label="Select single copy configuration">
-                        <option value="custom" selected="true">Single copy orthogroup custom</option>
-                        <option value="taxa">Minumum single copy taxa required in orthogroup</option>
+                <conditional name="specify_single_copy_cond">
+                    <param name="specify_single_copy" type="select" label="Specify single copy orthogroup selection?">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
                     </param>
-                    <when value="custom" />
-                    <when value="taxa">
-                        <param name="single_copy_taxa" type="integer" value="20" label="Minumum single copy taxa required in orthogroup"/>
-                        <param name="taxa_present" type="integer" value="21" label="Minumum taxa required in single copy orthogroup"/>
+                    <when value="no"/>
+                    <when value="yes">
+                        <conditional name="single_copy_cond">
+                            <param name="single_copy" type="select" label="Select single copy configuration">
+                                <!--
+                                FixMe: single_copy_custom is not currently supported because the
+                                ~/config/*.singleCopy.config files are not easy to manage by a suer
+                                and the GeneFamilyClassifier pipeline must be enhanced to provide an
+                                optional parameter for the hard-coded path to the config.
+                                <option value="custom" selected="true">Single copy orthogroup custom</option>
+                                -->
+                                <option value="taxa">Minumum single copy taxa required in orthogroup</option>
+                            </param>
+                            <when value="custom" />
+                            <when value="taxa">
+                                <param name="single_copy_taxa" type="integer" value="20" label="Minumum single copy taxa required in orthogroup"/>
+                                <param name="taxa_present" type="integer" value="21" label="Minumum taxa required in single copy orthogroup"/>
+                            </when>
+                        </conditional>
                     </when>
                 </conditional>
                 <conditional name="create_orthogroup_cond">
@@ -177,6 +210,9 @@
         <data name="output_ptcgfcs" format="ptcgfcs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'yes'</filter>
         </data>
+        <data name="output_ptsco" format="ptsco" label="Single copy orthogroup on ${on_string}">
+            <filter>options_type['options_type_selector'] == 'advanced' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
+        </data>
         <collection name="orthos" type="list">
             <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
         </collection>