Tool for changing case

scripts/taxonomy/readme.txt

@@ -4,7 +4,7 @@ How to prepare NCBI taxonomy for Galaxy Metagenomic Toolkit
 1. run runTest.sh
    If this script produces NO messages -> everything is OK
    
-2. run processRaxonomy.sh
+2. run processTaxonomy.sh
    This script does several things:
    - downloads taxonomy dump tarball from NCBI ftp site
    - downloads very large gi2taxId files for nucleotide and protein entries of GenBank

scripts/taxonomy/tax2_Node2Name.py

@@ -106,6 +106,7 @@ def main():
 #             contains a single 'scientific name' type
             try:
                 if field[2] == 'scientific name':
+                    field[1] = field[1].replace('\t','_')
                     sqlTemplate = string.Template('insert into names values($taxId, "$name", "$syn")')
                     sql = sqlTemplate.substitute(taxId = int(field[0]), name = field[1], syn = field[2])  
                     cur.execute(sql)

tool_conf.xml.sample

@@ -35,6 +35,7 @@
     <tool file="filters/Convert_characters1/1.0.0/convert_characters.xml" />
     <tool file="filters/createInterval/1.0.0/CreateInterval.xml" />
     <tool file="filters/Cut1/1.0.0/cutWrapper.xml" />
+    <tool file="filters/ChangeCase1/1.0.0/changeCase.xml" />
     <tool file="filters/Paste1/1.0.0/pasteWrapper.xml" />
     <tool file="filters/Remove_beginning1/1.0.0/remove_beginning.xml" />
     <tool file="filters/Show_beginning1/1.0.0/headWrapper.xml" />

tools/filters/ChangeCase1/1.0.0/changeCase.pl

@@ -0,0 +1,25 @@
+#! /usr/bin/perl -w
+
+use strict;
+use warnings;
+
+
+# Changes case to upper or lower in specified columns
+# changeCase.pl [filename] [output] [upper|lower]
+
+die "Check arguments\n" unless @ARGV == 3;
+
+open (IN,  "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n";
+open (OUT, ">$ARGV[1]") or die "Cannot create $ARGV[1]:$!\n";
+
+while (<IN>) {
+        if ($ARGV[2] eq "up") {
+                print OUT uc($_);
+        } elsif ($ARGV[2] eq "lo") {
+                print OUT lc($_);
+        }
+}
+
+close IN;
+close OUT;
+    

tools/filters/ChangeCase1/1.0.0/changeCase.xml

@@ -0,0 +1,30 @@
+<tool id="ChangeCase1" name="Change Case">
+  <description>to upper or lower</description>
+  <command interpreter="perl">changeCase.pl $input $out_file1 "$upperLower"</command>
+  <inputs>
+    <param format="txt" name="input" type="data" label="Change"/>
+    <param name="upperLower" type="select" label="To">
+      <option value="up">Upper case</option>
+      <option value="lo">Lower case</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="1.txt"/>
+      <param name="upperLower" value="up"/>
+      <output name="out_file1" file="change-case.dat"/>
+    </test>
+  </tests>
+  <help>
+
+This tool changes case for lower to upper and vice versa.  
+
+.. class:: infomark
+
+If you want to change case on a specific column use this tool in combination with *Text Manipulation->Cut*
+
+</help>
+</tool>