diff tools/seq_rename/seq_rename.xml @ 3:e1398f2ba9fe draft default tip

v0.0.8 galaxy_sequence_utils dependency etc

--- a/tools/seq_rename/seq_rename.xml	Fri Oct 11 04:39:16 2013 -0400
+++ b/tools/seq_rename/seq_rename.xml	Thu Feb 02 11:49:03 2017 -0500
@@ -1,18 +1,19 @@
-<tool id="seq_rename" name="Rename sequences" version="0.0.4">
+<tool id="seq_rename" name="Rename sequences" version="0.0.8">
     <description>with ID mapping from a tabular file</description>
     <requirements>
-        <requirement type="package" version="1.62">biopython</requirement>
+        <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
+        <requirement type="package" version="1.67">biopython</requirement>
         <requirement type="python-module">Bio</requirement>
     </requirements>
-    <version_commmand interpreter="python">seq_rename.py --version</version_commmand>
-    <command interpreter="python">
-seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file
-    </command>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <version_command interpreter="python">seq_rename.py --version</version_command>
+    <command interpreter="python">
+seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file
+    </command>
     <inputs>
         <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." />
         <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
@@ -20,17 +21,7 @@
         <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing new sequence identifiers"/>
     </inputs>
     <outputs>
-        <data name="output_file" format="fasta" label="Renamed ${on_string}">
-            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
-            <change_format>
-                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
-		<when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
-		<when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
-		<when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
-		<when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
-		<when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
-            </change_format>
-        </data>
+        <data name="output_file" format_source="input_file" metadata_source="input_file" label="Renamed ${on_string}"/>
     </outputs>
     <tests>
         <test>
@@ -55,12 +46,17 @@
 new sequence file (of the same format) where the sequence identifiers have been
 renamed according to the specified columns in your tabular file.
 
+Any original description is preserved (N/A for the SFF file format).
+
 WARNING: If you have any duplicates in the input sequence file, you will still
 have duplicate sequences in the output.
 
 WARNING: If the tabular file has more than one new name for any old ID, the
 last one is used.
 
+WARNING: The old and new names in your tabular file should not contain white space.
+If they do, only the first word is used as the identifier.
+
 **References**
 
 If you use this Galaxy tool in work leading to a scientific publication please
@@ -81,4 +77,8 @@
 This tool is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename
     </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/bioinformatics/btp163</citation>
+    </citations>
 </tool>