Mercurial > repos > greg > gene_family_aligner

changeset 58:c2b9081064f0 draft

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Uploaded
author greg
date Fri, 13 Oct 2017 14:24:30 -0400
parents 9c9c2ea494ba
children 0e1041ee1926
files gene_family_aligner.xml
diffstat 1 files changed, 23 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/gene_family_aligner.xml	Mon Oct 09 08:56:27 2017 -0400
+++ b/gene_family_aligner.xml	Fri Oct 13 14:24:30 2017 -0400
@@ -61,8 +61,8 @@
             </when>
         </conditional>
         <param name="codon_alignments" type="select" label="Codon alignments">
-            <option value="yes" selected="true">Yes</option>
-            <option value="no">No</option>
+            <option value="no" selected="true">No</option>
+            <option value="yes">Yes</option>
         </param>
         <conditional name="remove_gappy_sequences_cond">
             <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration">
@@ -135,6 +135,26 @@
     </outputs>
     <tests>
         <test>
+            <param name="input">
+                <collection type="list">
+                <element name="3722.faa" value="3722.faa"/>
+                <element name="3722.fna" value="3722.fna"/>
+                <element name="38889.faa" value="38889.faa"/>
+                <element name="38889.fna" value="38889.fna"/>
+                <element name="39614.faa" value="39614.faa"/>
+                <element name="39614.fna" value="39614.fna"/>
+                </collection>
+            </param>
+            <output_collection name="primary_faa" type="list">
+                <element name="3722.faa.aln" file="3722.faa.aln" ftype="fasta"/>
+                <element name="38889.faa.aln" file="38889.faa.aln" ftype="fasta"/>
+                <element name="39614.faa.aln" file="39614.faa.aln" ftype="fasta"/>
+            </output_collection>
+            <output_collection name="primary_fna" type="list">
+                <element name="3722.fna.aln" file="3722.fna.aln" ftype="fasta"/>
+                <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/>
+                <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/>
+            </output_collection>
         </test>
     </tests>
     <help>
@@ -152,7 +172,7 @@
 
   - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations.
 
- * **Codon alignments** - select 'Yes' to create codon multiple sequence alignments.  This option requires protein and their corresponding coding sequences to be provided as input data.
+ * **Codon alignments** - select 'Yes' to create codon multiple sequence alignments.  This option requires both protein and their corresponding coding sequence orthogroup fasta files to be present in the GeneFamilyAligner input data that was produced by the GeneFamilyIntegrator.
 
 **Other options**