# HG changeset patch
# User greg
# Date 1504874006 14400
# Node ID ee70ebb1ca4e3f61434a13e6205c16f446fd4fbb
# Parent  31f85a5aefc0b88a4b25681df3f6691c63281598
Uploaded

diff -r 31f85a5aefc0 -r ee70ebb1ca4e gene_family_aligner.xml
--- a/gene_family_aligner.xml	Fri Sep 08 08:33:11 2017 -0400
+++ b/gene_family_aligner.xml	Fri Sep 08 08:33:26 2017 -0400
@@ -69,25 +69,41 @@
         <expand macro="cond_remove_gappy_sequences" />
     </inputs>
     <outputs>
-        <collection name="primary" type="list" label="${tool.name} (primary proteins orthogroup alignments) on ${on_string}">
-            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln" format="fasta" />
+        <collection name="primary_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_faa" format="fasta" />
             <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
         </collection>
-        <collection name="trimmed" type="list" label="${tool.name} (trimmed proteins orthogroup alignments) on ${on_string}">
-            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln" format="fasta" />
+        <collection name="primary_fna" type="list" label="${tool.name} (primary orthogroup codon alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_fna" format="fasta" />
+            <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
+        </collection>
+        <collection name="trimmed_faa" type="list" label="${tool.name} (trimmed orthogroup protein alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_faa" format="fasta" />
             <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
         </collection>
-        <collection name="primary_trimmed" type="list" label="${tool.name} (primary proteins orthogroup alignments) on ${on_string}">
+        <collection name="primary_trimmed" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}">
             <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
-            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
+            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter>
+        </collection>
+        <collection name="trimmed_fna" type="list" label="${tool.name} (trimmed orthogroup codon alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_fna" format="fasta" />
+            <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
         </collection>
-        <collection name="filtered" type="list" label="${tool.name} (filtered proteins orthogroup alignments) on ${on_string}">
-            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln" format="fasta" />
+        <collection name="primary_trimmed" type="list" label="${tool.name} (primary orthogroup protein and codon alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
+            <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter>
+        </collection>
+        <collection name="filtered" type="list" label="${tool.name} (filtered orthogroup protein alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_faa" format="fasta" />
             <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
         </collection>
         <collection name="primary_filtered" type="list" label="${tool.name} (primary and trimmed proteins orthogroup alignments) on ${on_string}">
             <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
-            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
+            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter>
+        </collection>
+        <collection name="filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" />
+            <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
         </collection>
     </outputs>
     <tests>