diff picard_NormalizeFasta.xml @ 0:4419e9980172 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_NormalizeFasta.xml	Thu Oct 23 12:03:34 2014 -0400
@@ -0,0 +1,73 @@
+<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="1.122.0">
+  <description>normalize fasta datasets</description>
+  <requirements>
+    <requirement type="package" version="1.122.0">picard</requirement>
+  </requirements>
+  
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  
+  <command>
+    @java_options@
+    
+  
+    ## Two lines below are due to the fact that picard likes fasta files to have extension .fa  
+    #set $fasta_file="local_fasta.fa"
+    ln -s "${inputFile}" "${fasta_file}" &amp;&amp;    
+    
+    java -jar \$JAVA_JAR_PATH/NormalizeFasta.jar
+    
+    INPUT="${fasta_file}"
+    OUTPUT="${outFile}"
+    LINE_LENGTH="${line_length}"
+    TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
+    
+    QUIET=true
+    VERBOSITY=ERROR
+  
+  </command>
+  <inputs>
+    <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" />
+    <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
+    <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
+  </inputs> 
+  
+  <outputs>
+    <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
+      <param name="line_length" value="40"/>
+      <param name="truncate_sequence_names_at_whitespaces" value="False"/>
+      <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
+    </test>
+  </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <help>
+
+**Purpose**
+
+Takes any dataset that conforms to the fasta format and normalizes it so that all lines of sequence except the last line per named sequence are of the same length.
+
+@dataset_collections@
+
+@description@
+
+  LINE_LENGTH=Integer           The line length to be used for the output fasta file.  Default value: 100. 
+  
+  TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean
+                                Truncate sequence names at first whitespace.  Default value: false. Possible values: {true, false} 
+
+@more_info@
+
+  </help>
+</tool>
+
+