Mercurial > repos > devteam > fastx_artifacts_filter

changeset 2:b664e561b28f draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:40:24 -0400
parents 8dfa8ecd0191
children ecfaafccf192
files fastx_artifacts_filter.xml tool_dependencies.xml
diffstat 2 files changed, 30 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/fastx_artifacts_filter.xml	Tue Nov 26 12:45:42 2013 -0500
+++ b/fastx_artifacts_filter.xml	Tue Oct 13 12:40:24 2015 -0400
@@ -1,36 +1,36 @@
 <tool id="cshl_fastx_artifacts_filter" version="1.0.0" name="Remove sequencing artifacts">
-	<description></description>
-	<requirements>
+    <description></description>
+    <requirements>
         <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
     </requirements>
-	<command>zcat -f '$input' | fastx_artifacts_filter -v -o "$output"
+    <command>
+<![CDATA[
+zcat -f < '$input' | fastx_artifacts_filter -v -o '$output'
 #if $input.ext == "fastqsanger":
--Q 33
+    -Q 33
 #end if
-	</command>
-
-	<inputs>
-		<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" />
-
-	</inputs>
+]]>
+    </command>
 
-	<tests>
-		<test>
-			<!-- Filter FASTA file -->
-			<param name="input" value="fastx_artifacts1.fasta" /> 
-			<output name="output" file="fastx_artifacts1.out" />
-		</test>
-		<test>
-			<!-- Filter FASTQ file -->
-			<param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" />
-			<output name="output" file="fastx_artifacts2.out" />
-		</test>
-	</tests>
-
-	<outputs>
-		<data format="input" name="output" metadata_source="input" />
-	</outputs>
-<help>
+    <inputs>
+        <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" />
+    </inputs>
+    <outputs>
+        <data format_source="input" name="output" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- Filter FASTA file -->
+            <param name="input" value="fastx_artifacts1.fasta" />
+            <output name="output" ftype="fasta" file="fastx_artifacts1.out" />
+        </test>
+        <test>
+            <!-- Filter FASTQ file -->
+            <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" />
+            <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" />
+        </test>
+    </tests>
+    <help>
 **What it does**
 
 This tool filters sequencing artifacts (reads with all but 3 identical bases).
@@ -81,12 +81,12 @@
     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA
     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA
     AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA
-    
+
 ------
 
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-</help>
+    </help>
 <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
 </tool>
--- a/tool_dependencies.xml	Tue Nov 26 12:45:42 2013 -0500
+++ b/tool_dependencies.xml	Tue Oct 13 12:40:24 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>