Mercurial > repos > devteam > fastx_barcode_splitter

changeset 3:3b0cd3132ddc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:40:38 -0400
parents 1a20fbb8bad8
children e3d91cb9f196
files fastx_barcode_splitter.xml fastx_barcode_splitter_galaxy_wrapper.sh tool_dependencies.xml
diffstat 3 files changed, 35 insertions(+), 40 deletions(-) [+]
line wrap: on
line diff
--- a/fastx_barcode_splitter.xml	Tue Jun 03 14:50:06 2014 -0400
+++ b/fastx_barcode_splitter.xml	Tue Oct 13 12:40:38 2015 -0400
@@ -1,42 +1,38 @@
 <tool id="cshl_fastx_barcode_splitter" version="1.0.0" name="Barcode Splitter">
-	<description></description>
+    <description></description>
     <requirements>
         <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
     </requirements>
-	<command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command>
+    <command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' </command>
+
+    <inputs>
+        <param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
+        <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
 
-	<inputs>
-		<param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
-		<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
+        <param name="EOL" type="select" label="Barcodes found at">
+            <option value="--bol">Start of sequence (5' end)</option>
+            <option value="--eol">End of sequence (3' end)</option>
+        </param>
 
-		<param name="EOL" type="select" label="Barcodes found at">
-			<option value="--bol">Start of sequence (5' end)</option>
-			<option value="--eol">End of sequence (3' end)</option>
-		</param>
+        <param name="mismatches" type="integer" value="2" label="Number of allowed mismatches" />
 
-		<param name="mismatches" type="integer" size="3" value="2" label="Number of allowed mismatches" />
-		
-		<param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
-	
-	</inputs>
-	
-	<tests>
-		<test>
-			<!-- Split a FASTQ file -->
-			<param name="BARCODE" value="fastx_barcode_splitter1.txt" />
-			<param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
-			<param name="EOL" value="Start of sequence (5' end)" />
-			<param name="mismatches" value="2" />
-			<param name="partial" value="0" />
-			<param name="output" file="fastx_barcode_splitter1.out" />
-		</test>
-	</tests>
-
-	<outputs>
-		<data format="html" name="output" />
-	</outputs>
-<help>
-
+        <param name="partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" />
+    </inputs>
+    <outputs>
+        <data format="html" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- Split a FASTQ file -->
+            <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
+            <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
+            <param name="EOL" value="Start of sequence (5' end)" />
+            <param name="mismatches" value="2" />
+            <param name="partial" value="0" />
+            <output name="output" file="fastx_barcode_splitter1.out" />
+        </test>
+    </tests>
+    <help>
 **What it does**
 
 This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria.
@@ -50,11 +46,11 @@
 Example::
 
     #This line is a comment (starts with a 'number' sign)
-    BC1	GATCT
-    BC2	ATCGT
-    BC3	GTGAT
+    BC1    GATCT
+    BC2    ATCGT
+    BC3    GTGAT
     BC4 TGTCT
-    
+
 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
 Sequences matching the barcode will be stored in the appropriate file.
 
@@ -72,7 +68,6 @@
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
- 
-</help>
+    </help>
 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
 </tool>
--- a/fastx_barcode_splitter_galaxy_wrapper.sh	Tue Jun 03 14:50:06 2014 -0400
+++ b/fastx_barcode_splitter_galaxy_wrapper.sh	Tue Oct 13 12:40:38 2015 -0400
@@ -62,7 +62,7 @@
 PREFIX="$BASEPATH""${LIBNAME}__"
 SUFFIX=".txt"
 
-RESULTS=`zcat -f "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"`
+RESULTS=`zcat -f < "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"`
 if [ $? != 0 ]; then
 	echo "error"
 fi
--- a/tool_dependencies.xml	Tue Jun 03 14:50:06 2014 -0400
+++ b/tool_dependencies.xml	Tue Oct 13 12:40:38 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="fastx_toolkit" version="0.0.13">
-        <repository changeset_revision="1cd326991d32" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="e76e81b3eccf" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>