changeset 78:da6a3f55771e draft

Deleted selected files

--- a/picard_NormalizeFasta.xml	Wed Feb 19 23:10:37 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
-<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="1.106.0">
-<description>Takes any file 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.</description>
-<requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
-  <command interpreter="java -jar -Xmx8g">
-      $JAVA_JAR_PATH/NormalizeFasta.jar
-
-          #if str( $OUTPUT ):
-              OUTPUT="${OUTPUT}"
-          #end if
-          #if str( $LINE_LENGTH ):
-              LINE_LENGTH="${LINE_LENGTH}"
-          #end if
-          #if str( $TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE ):
-              TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE}"
-          #end if
-
-      VALIDATION_STRINGENCY=LENIENT
-      QUIET=True
-      TMP_DIR="${__new_file_path__}" 
-  </command>
-  
-  <stdio>
-    <exit_code range="0" level="warning" description="Tool finished correctly" />
-  </stdio>
-  
-  <inputs>
-       <param name="title" label="Name for the output fasta file" type="text" default="output" />
-      <param format="fasta" name="OUTPUT" type="data" label="The output fasta file to write. Required." help="" />
-      <param name="LINE_LENGTH" type="integer" value="100" label="The line length to be used for the output fasta file. Default value: 100. This option can be set to 'null' to clear the default value." help="" />
-      <param name="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE" type="boolean" label="Truncate sequence names at first whitespace. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
-  </inputs>
-  <outputs>
-    <data format="fasta" name="output1" label="${title}.fasta" >
-    </data>
-  </outputs>
- <!-- <tests>
-  <test> -->
-     <!-- Here is a command line that works:
-        java -jar ...
-     -->
- <!--     <param name="inputFile" value="XXCHANGEMEE-input" />
-      <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" />
-    </test>
-  </tests> -->
-  <help>
-Picard documentation says:
-
-  
-NormalizeFasta
-
-Takes any file 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.
-Option	Description
-INPUT=File	The input fasta file to normalize. Required.
-OUTPUT=File	The output fasta file to write. Required.
-LINE_LENGTH=Integer	The line length to be used for the output fasta file. Default value: 100. This option can be set to 'null' to clear the default value.
-TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean	Truncate sequence names at first whitespace. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} 
-
-
-  </help>
-</tool>