changeset 1:d533e4b75800 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155

--- a/replaceColumn.xml	Fri Feb 24 10:14:15 2017 -0500
+++ b/replaceColumn.xml	Sun Sep 23 04:03:34 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="replace_column_with_key_value_file" name="Replace column" version="0.1">
+<tool id="replace_column_with_key_value_file" name="Replace column" version="0.2">
     <description>by values which are defined in a convert file</description>
     <command>
         <![CDATA[
@@ -14,35 +14,39 @@
 original_file = '$original_file'
 column = int("$column_replace") - 1
 ignore_start_lines = int("$skip_lines")
-delimiter_local = "\t" if str("$delimiter") == "" else str("$delimiter")
+delimiter_local = "\t" if str("$delimiter") == "tab" else str("$delimiter")
+comment_str = str("$pass_comments")
+unk_strat = str("$unknowns_strategy")
 
-## read conversion information to index 
+## read conversion information to index
 conversion = {}
 
 with open(replace_file, 'r') as conversion_file:
     for line in conversion_file:
         conv_key_value = line.strip().split()
         if len(conv_key_value) == 2:
-            conversion[conv_key_value[0]] = conv_key_value[1]                
+            conversion[conv_key_value[0]] = conv_key_value[1]
 
 ## read file line by line, search for column entry if it can be replaced. Otherwise it will be skipped.
 with open("output_file", 'w') as output:
     with open(original_file) as original:
         for i, line in enumerate(original):
-            if i < ignore_start_lines:
+            if i < ignore_start_lines or (comment_str and line.startswith(comment_str)):
                 output.write(line)
                 continue
 
-            if str("$delimiter") == "":
-                line_content = line.split()
-            else:
-                line_content = line.split(str("$delimiter"))
+            line_content = line.rstrip().split(delimiter_local)
 
             out = list()
             for j, line_content_column in enumerate(line_content):
                 if j == column:
+
                     if line_content_column in conversion:
                         out.append(conversion[line_content_column])
+                    elif unk_strat == "print":
+                        out.append(line_content_column)
+                    elif unk_strat == "error":
+                        raise Exception('ERROR: Encountered a value [%s] in the file that is not in the replacements file and is not commented with [%s]' % (line_content_column, comment_str))
                 else:
                     out.append(line_content_column)
 
@@ -63,14 +67,26 @@
                label="Which column should be replaced?" />
         <param name="skip_lines" type='integer' value='0' label="Skip this many starting lines" />
         <param name="delimiter" type="select" label="Delimited by">
-            <option value="" selected="True">Tab</option>
-            <option value=" ">Whitespace</option>
+            <option value="tab" selected="True">Tab</option>
+            <option value=" ">Space</option>
             <option value=".">Dot</option>
             <option value=",">Comma</option>
             <option value="-">Dash</option>
             <option value="_">Underscore</option>
             <option value="|">Pipe</option>
         </param>
+        <param name="unknowns_strategy" type="select" label="When an unknown value is encountered">
+            <option value="skip" selected="True">Skip / Do not print</option>
+            <option value="print">Print without modification</option>
+            <option value="error">Exit with an error</option>
+        </param>
+        <param name="pass_comments" type="text" value="#" label="Do not perform replacement on lines starting with">
+            <sanitizer>
+                <valid>
+                    <add value="#" />
+                </valid>
+            </sanitizer>
+        </param>
     </inputs>
     <outputs>
         <data  name="outfile_replace" format="txt" from_work_dir="output_file"/>
@@ -81,7 +97,9 @@
             <param name="original_file" value="original_file" ftype="tabular" />
             <param name="column_replace" value="1"/>
             <param name="skip_lines" value="1"/>
-            <param name="delimiter" value="" />
+            <param name="delimiter" value="tab" />
+            <param name="unknowns_strategy" value="skip"/>
+            <param name="pass_comments" value="#"/>
             <output name="outfile_replace" file="result_file"/>
         </test>
         <test>
@@ -89,16 +107,37 @@
             <param name="original_file" value="empty_mapping" ftype="tabular" />
             <param name="column_replace" value="1"/>
             <param name="skip_lines" value="1"/>
-            <param name="delimiter" value="" />
+            <param name="delimiter" value="tab" />
+            <param name="unknowns_strategy" value="skip"/>
+            <param name="pass_comments" value="#"/>
             <output name="outfile_replace" file="result_file_empty_mapping"/>
         </test>
+        <test expect_failure="True">
+            <param name="replace_information" value="neg_test_map.txt" ftype="tabular" />
+            <param name="original_file" value="neg_test_commented.txt" ftype="tabular" />
+            <param name="column_replace" value="1"/>
+            <param name="skip_lines" value="0"/>
+            <param name="delimiter" value="tab" />
+            <param name="unknowns_strategy" value="error"/>
+            <param name="pass_comments" value="#"/>
+        </test>
+        <test>
+            <param name="replace_information" value="neg_test_map.txt" ftype="tabular" />
+            <param name="original_file" value="neg_test_commented.txt" ftype="tabular" />
+            <param name="column_replace" value="1"/>
+            <param name="skip_lines" value="0"/>
+            <param name="delimiter" value="tab" />
+            <param name="unknowns_strategy" value="print"/>
+            <param name="pass_comments" value="#"/>
+            <output name="outfile_replace" file="neg_test_commented.txt"/>
+        </test>
     </tests>
     <help>
         <![CDATA[
 **What it does**
 
-This tool replaces the entries of a defined column with entries given by a replacement file. 
-For example the replacement file holds the information of the naming scheme of ensembl annotated chromosomes in the frist column and in the second the UCSC annotation. 
+This tool replaces the entries of a defined column with entries given by a replacement file.
+For example the replacement file holds the information of the naming scheme of ensembl annotated chromosomes in the frist column and in the second the UCSC annotation.
 A file which is having information about chromosomes in ensembl notation in column x can now be converted to a file which holds the same information but in UCSC annotation.
 
 A useful repository for ensembl and UCSC chromosomes mapping is: https://github.com/dpryan79/ChromosomeMappings

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/neg_test_commented.txt	Sun Sep 23 04:03:34 2018 -0400
@@ -0,0 +1,2 @@
+#test
+NC_000964.33	should not match

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/neg_test_map.txt	Sun Sep 23 04:03:34 2018 -0400
@@ -0,0 +1,1 @@
+NC_000964.3	Chromosome

--- a/test-data/original_file	Fri Feb 24 10:14:15 2017 -0500
+++ b/test-data/original_file	Sun Sep 23 04:03:34 2018 -0400
@@ -1,51 +1,51 @@
 track type="bedGraph" description="BT089 CpG merged methylation fractions"
-1       10468   10470   0.209302
-1       10470   10472   0.611111
-1       10483   10485   0.428571
-1       10488   10490   0.846154
-1       10492   10494   0.666667
-1       10496   10498   0.916667
-1       10524   10526   0.916667
-1       10541   10543   0.818182
-1       10562   10564   0.615385
-1       10570   10572   0.916667
-1       10576   10578   0.615385
-1       10578   10580   0.538462
-1       10588   10590   0.909091
-1       10608   10610   0.700000
-1       10616   10618   0.875000
-1       10619   10621   0.714286
-1       10630   10632   0.428571
-1       10632   10634   0.444444
-1       10635   10637   0.400000
-1       10637   10639   0.400000
-1       10640   10642   0.900000
-1       10643   10645   0.600000
-1       10649   10651   0.727273
-1       10659   10661   0.857143
-1       10661   10663   0.428571
-1       10664   10666   0.846154
-1       10666   10668   0.750000
-1       10669   10671   0.916667
-1       10672   10674   0.916667
-1       10678   10680   1.000000
-1       10688   10690   0.900000
-1       10690   10692   0.545455
-1       10693   10695   1.000000
-1       10695   10697   0.909091
-1       10698   10700   0.916667
-1       10701   10703   1.000000
-1       10707   10709   1.000000
-1       10717   10719   0.866667
-1       10719   10721   0.692308
-1       10722   10724   1.000000
-1       10724   10726   0.933333
-1       10727   10729   0.933333
-1       10730   10732   1.000000
-1       10736   10738   0.933333
-1       10746   10748   0.857143
-1       10748   10750   0.500000
-1       10751   10753   0.928571
-1       10753   10755   0.857143
-1       10756   10758   1.000000
-1       10759   10761   0.857143
[phone]	0.209302
[phone]	0.611111
[phone]	0.428571
[phone]	0.846154
[phone]	0.666667
[phone]	0.916667
[phone]	0.916667
[phone]	0.818182
[phone]	0.615385
[phone]	0.916667
[phone]	0.615385
[phone]	0.538462
[phone]	0.909091
[phone]	0.700000
[phone]	0.875000
[phone]	0.714286
[phone]	0.428571
[phone]	0.444444
[phone]	0.400000
[phone]	0.400000
[phone]	0.900000
[phone]	0.600000
[phone]	0.727273
[phone]	0.857143
[phone]	0.428571
[phone]	0.846154
[phone]	0.750000
[phone]	0.916667
[phone]	0.916667
[phone]	1.000000
[phone]	0.900000
[phone]	0.545455
[phone]	1.000000
[phone]	0.909091
[phone]	0.916667
[phone]	1.000000
[phone]	1.000000
[phone]	0.866667
[phone]	0.692308
[phone]	1.000000
[phone]	0.933333
[phone]	0.933333
[phone]	1.000000
[phone]	0.933333
[phone]	0.857143
[phone]	0.500000
[phone]	0.928571
[phone]	0.857143
[phone]	1.000000
[phone]	0.857143