Few of cosmetic changes

tools/extract/extractAxt_wrapper.xml

@@ -24,6 +24,13 @@
     </tests>
     <help>
 
+.. class:: warningmark
+
+**IMPORTANT**: AXT formatted alignments will be phased out from Galaxy in the coming weeks. They will be replaced with pairwise MAF alignments, which are already available. To try pairwise MAF alignments use "Extract Pairwise MAF blocks" tool in *Fetch Sequences and Alignments* section.
+
+--------
+
+
 .. class:: infomark
 
 **TIP:** The last field of the axt header is the same as the column 4 (name) of the corresponding BED file.  *This is very useful* for establishing correspondence between alignments and the original BED file.

tools/extract/fasta-subseq-wrapper.pl

@@ -19,6 +19,7 @@ my @locFields = ();
 my %seqLocation = ();
 
 die "Cannot fetch sequences for unspecified genome\n" unless @ARGV == 11;
+die "Please specify genome build by clicking on pencil icon in the original dataset\n" if $ARGV[10] =~ m/\?/;
 
 # Read /depot/data2/galaxy/alignseq.loc
 

tools/extract/fasta-subseq-wrapper.xml

@@ -17,7 +17,7 @@
 
 .. class:: warningmark
 
-Make sure the input data has been specified a database build. 
+Make sure that the genome build is specified for the interval dataset you are extracting sequences for (click the pencil icon if it is not specified). However, if the build is specified and the tool still gives you an error, your genome of interest may only be partially assembled (ie, in scaffolds).  To extract sequences from such partially assembled genomes use *Extract Genomic DNA from unassmebled genomes* tool.
 
 -----
 

tools/filters/axt_to_concat_fasta.xml

@@ -23,6 +23,12 @@
     </tests>
     <help>
 
+.. class:: warningmark
+
+**IMPORTANT**: AXT formatted alignments will be phased out from Galaxy in the coming weeks. They will be replaced with pairwise MAF alignments, which are already available. To try pairwise MAF alignments use "Extract Pairwise MAF blocks" tool in *Fetch Sequences and Alignments* section.
+
+--------
+
 **Syntax**
 
 This tool converts an AXT formated file to the FASTA format, and concatenates the results in the same build.

tools/filters/axt_to_fasta.xml

@@ -22,6 +22,13 @@
     </tests>
     <help>
 
+.. class:: warningmark
+
+**IMPORTANT**: AXT formatted alignments will be phased out from Galaxy in the coming weeks. They will be replaced with pairwise MAF alignments, which are already available. To try pairwise MAF alignments use "Extract Pairwise MAF blocks" tool in *Fetch Sequences and Alignments* section.
+
+--------
+
+
 **Syntax**
 
 This tool converts an AXT formated file to the FASTA format.

tools/filters/axt_to_lav.xml

@@ -19,6 +19,13 @@
   </outputs>
     <help>
 
+.. class:: warningmark
+
+**IMPORTANT**: AXT formatted alignments will be phased out from Galaxy in the coming weeks. They will be replaced with pairwise MAF alignments, which are already available. To try pairwise MAF alignments use "Extract Pairwise MAF blocks" tool in *Fetch Sequences and Alignments* section.
+
+--------
+
+
 **Syntax**
 
 This tool converts an AXT formated file to the LAV format.

tools/filters/compare.xml

@@ -3,8 +3,8 @@
   <command interpreter="perl">joinWrapper.pl $input1 $input2 $field1 $field2 $mode "Y" $out_file1</command>
   <inputs>
     <page>
-      <param format="tabular" name="input1" type="data" label="of Query1"/>
-      <param format="tabular" name="input2" type="data" label="of Query2" help="Click [Next Step] to select columns and return type" />
+      <param format="tabular" name="input1" type="data" label="Compare"/>
+      <param format="tabular" name="input2" type="data" label="against" help="Click [Next Step] to select columns and return type" />
     </page>
     <page>
       <param name="field1" label="Using column" size="4" type="select" dynamic_options="get_available_columns( input1.file_name )" help="of First query"/>

tools/filters/joiner.xml

@@ -38,7 +38,7 @@
 
 **Syntax**
 
-This tool joins lines of two queries on a common field, which is similarly to unix join command and SQL join operation. 
+This tool joins lines of two queries on a common field similarly to unix join command or the SQL join operation. 
 
 - Columns are referenced with a **number**. For example, **3** refers to the 3rd column of a tab-delimited file.
 

tools/visualization/build_ucsc_custom_track.xml

@@ -76,7 +76,7 @@ This tool displays the selected datasets with their custom track attributes (if
 
 This tool allows you to set the **Color** and **Visibility** attributes and you can edit the **Name** attribute of the dataset by clicking on **"edit attributes"** button (pencil icon) next to the dataset name in the history panel. 
 
-Please note that the primary dataset in step 1 of the tool sets the database build for the datasets in step 2.
+Please note that the primary dataset in step 1 of the tool sets the database build for the datasets in following steps. For example, if your first dataset belogs to hg18, you will only be able to select hg18 associated datasets on the next step.
 
 	</help>