# HG changeset patch
# User greg
# Date 1493384582 14400
# Node ID 9531bbe2d8ff1c5364c7aa75f9be0473fe91148d
# Parent  61977f3f19eaf2f9a6723581fbbbcfc68905a6c3
Uploaded

diff -r 61977f3f19ea -r 9531bbe2d8ff macros.xml
--- a/macros.xml	Thu Apr 27 10:23:48 2017 -0400
+++ b/macros.xml	Fri Apr 28 09:03:02 2017 -0400
@@ -59,13 +59,13 @@
         </param>
     </xml>
     <xml name="param_orthogroup_fna">
-        <param name="orthogroup_fna" type="select" label="Process corresponding gene family classification orthogroups CDS fasta files?">
+        <param name="orthogroup_fna" type="select" label="Orthogroups coding sequences?">
             <option value="yes" selected="true">Yes</option>
             <option value="no">No</option>
         </param>
     </xml>
     <xml name="param_scaffold">
-        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
+        <param name="scaffold" type="select" label="Gene family 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>
@@ -78,9 +78,9 @@
     </xml>
     <xml name="cond_alignment_method">
         <conditional name="alignment_method_cond">
-            <param name="alignment_method" type="select" force_select="true" label="Select method for multiple sequence alignments">
-                <option value="mafft" selected="true">MAFFT algorithm</option>
-                <option value="pasta">PASTA algorithm</option>
+            <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
+                <option value="mafft" selected="true">MAFFT</option>
+                <option value="pasta">PASTA</option>
             </param>
             <when value="mafft" />
             <when value="pasta">
@@ -90,31 +90,31 @@
     </xml>
     <xml name="cond_remove_gappy_sequences">
         <conditional name="remove_gappy_sequences_cond">
-            <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
+            <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration?">
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
             <when value="no" />
             <when value="yes">
                 <conditional name="trim_type_cond">
-                    <param name="trim_type" type="select" label="Select process used for trimming">
-                        <option value="gap_trimming" selected="true">Remove gappy sites in alignments (gap trimming)</option>
-                        <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach (automated trimming)</option>
+                    <param name="trim_type" type="select" label="Trimming method">
+                        <option value="gap_trimming" selected="true">Gap score based trimming</option>
+                        <option value="automated_trimming">Automated heuristic trimming</option>
                     </param>
                     <when value="gap_trimming">
-                        <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Remove sites in alignments with gaps of" />
+                        <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" />
                     </when>
                     <when value="automated_trimming" />
                 </conditional>
                 <conditional name="remove_sequences_with_gaps_cond">
-                    <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
+                    <param name="remove_sequences_with_gaps" type="select" label="Remove sequences?">
                         <option value="no" selected="true">No</option>
                         <option value="yes">Yes</option>
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Remove sequences with gaps of" />
-                        <param name="iterative_realignment" type="integer" optional="true" min="0" label="Maximum number of iterations" />
+                        <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" />
+                        <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
                     </when>
                 </conditional>
             </when>
@@ -130,34 +130,4 @@
             url = {https://github.com/dePamphilis/PlantTribes},}
         </citation>
     </xml>
-    <xml name="citations2to4">
-        <citation type="bibtex">
-            @article{Sasidharan2012,
-            journal = {Nucleic Acids Research},
-            author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
-            title = {GFam: a platform for automatic annotation of gene families},
-            year = {2012},
-            pages = {gks631},}
-        </citation>
-        <citation type="bibtex">
-            @article{Li2003,
-            journal = {Genome Research}
-            author = {3. Li L, Stoeckert CJ, Roos DS},
-            title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
-            year = {2003},
-            volume = {13},
-            number = {9},
-            pages = {2178-2189},}
-        </citation>
-        <citation type="bibtex">
-            @article{Emms2015,
-            journal = {Genome Biology}
-            author = {4. Emms DM, Kelly S},
-            title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
-            year = {2015},
-            volume = {16},
-            number = {1},
-            pages = {157},}
-        </citation>
-    </xml>
 </macros>