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changeset 0:9cb372481a71

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Uploaded tool tarball.
author devteam
date Wed, 25 Sep 2013 11:21:27 -0400
parents
children d77c9c6ecf68
files fastx_trimmer.xml test-data/fastx_trimmer1.fasta test-data/fastx_trimmer1.out test-data/fastx_trimmer2.fastq test-data/fastx_trimmer2.out tool_dependencies.xml
diffstat 6 files changed, 113 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastx_trimmer.xml	Wed Sep 25 11:21:27 2013 -0400
@@ -0,0 +1,83 @@
+<tool id="cshl_fastx_trimmer" version="1.0.0" name="Trim sequences">
+	<description></description>
+    <requirements>
+        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
+    </requirements>
+	<command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output
+#if $input.ext == "fastqsanger":
+-Q 33
+#end if
+	</command>
+
+	<inputs>
+		<param format="fasta,fastqsolexa,fastqsanger" version="1.0.0" name="input" type="data" label="Library to clip" />
+
+		<param version="1.0.0" name="first" size="4" type="integer" value="1">
+			<label>First base to keep</label>
+		</param>
+
+		<param version="1.0.0" name="last" size="4" type="integer" value="21">
+			<label>Last base to keep</label>
+		</param>
+	</inputs>
+
+	<tests>
+		<test>
+			<!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
+			<param version="1.0.0" name="input" value="fastx_trimmer1.fasta" />
+			<param version="1.0.0" name="first" value="5"/>
+			<param version="1.0.0" name="last" value="36"/>
+			<output version="1.0.0" name="output" file="fastx_trimmer1.out" />
+		</test>
+		<test>
+			<!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
+			<param version="1.0.0" name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
+			<param version="1.0.0" name="first" value="1"/>
+			<param version="1.0.0" name="last" value="27"/>
+			<output version="1.0.0" name="output" file="fastx_trimmer2.out" />
+		</test>
+	</tests>
+
+	<outputs>
+		<data format="input" version="1.0.0" name="output" metadata_source="input" />
+	</outputs>
+	<help>
+**What it does**
+
+This tool trims (cut bases from) sequences in a FASTA/Q file.
+  
+--------
+
+**Example**
+
+Input Fasta file (with 36 bases in each sequences)::
+
+    >1-1
+    TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
+    >2-1
+    CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
+    
+
+Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
+
+    >1-1
+    TATGGTCAGAAACCATATGCA
+    >2-1
+    CAGCGAGGCTTTAATGCCATT
+
+Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences::
+
+    >1-1
+    TCAGA
+    >2-1
+    AGGCT
+    
+    ------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    
+</help>
+<!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_trimmer1.fasta	Wed Sep 25 11:21:27 2013 -0400
@@ -0,0 +1,4 @@
+>CSHL__2_FC042NGABCD:8:1:120:202
+ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
+>CSHL__2_FC042NGABCD:8:1:103:1185
+ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_trimmer1.out	Wed Sep 25 11:21:27 2013 -0400
@@ -0,0 +1,4 @@
+>CSHL__2_FC042NGABCD:8:1:120:202
+TAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
+>CSHL__2_FC042NGABCD:8:1:103:1185
+CGATAGATCGGCAGAGCTCGTTTACCGTCTTC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_trimmer2.fastq	Wed Sep 25 11:21:27 2013 -0400
@@ -0,0 +1,8 @@
+@CSHL__2_FC042NGABCD:8:1:120:202
+ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
++CSHL__2_FC042NGABCD:8:1:120:202
+40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8
+@CSHL__2_FC042NGABCD:8:1:103:1185
+ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
++CSHL__2_FC042NGABCD:8:1:103:1185
+40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_trimmer2.out	Wed Sep 25 11:21:27 2013 -0400
@@ -0,0 +1,8 @@
+@CSHL__2_FC042NGABCD:8:1:120:202
+ACGATAGATCGGAAGAGCTAGTATGCC
++CSHL__2_FC042NGABCD:8:1:120:202
+40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1
+@CSHL__2_FC042NGABCD:8:1:103:1185
+ATCACGATAGATCGGCAGAGCTCGTTT
++CSHL__2_FC042NGABCD:8:1:103:1185
+40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 0 9 22 17 14 8 36 15 34 22 12 23
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 25 11:21:27 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="fastx_toolkit" version="0.0.13">
+        <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>