diff extract_bcs.xml @ 0:ce2477cd3d95 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_bcs.xml	Tue Nov 14 05:53:20 2017 -0500
@@ -0,0 +1,48 @@
+<tool id="bctools_extract_barcodes" name="Extract barcodes" version="@VERSION@">
+    <description>according to pattern</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        extract_bcs.py
+        '$reads'
+        #if $barcode_pattern and $barcode_pattern is not None:
+            '$barcode_pattern'
+        #end if
+        --bcs '$extracted_barcodes'
+        > '$reads_cleaned'
+    ]]></command>
+    <inputs>
+        <param name="reads" type="data" format="fastq" label="Barcoded sequences" />
+        <param name="barcode_pattern" type="text" label="Pattern for extracting barcode nucleotides" help="Starting at 5'-end. X positions will be moved to a separate file, N positions will be kept.">
+            <sanitizer invalid_char="N">
+                <valid initial="none">
+                    <add value="X"/>
+                    <add value="N"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="reads_cleaned" format="fastq"/>
+        <data name="extracted_barcodes" format="fastq"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reads" value="reads.fastq"/>
+            <param name="barcode_pattern" value="XXXNNXXX"/>
+            <output name="reads_cleaned" file="result_original_head.fastq"/>
+            <output name="extracted_barcodes" file="extracted_bcs.fastq"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+bctools - Extract barcodes according to pattern
+===============================================
+
+Exract barcodes from a FASTQ file according to a user-specified pattern and write them to a separate FASTQ file.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>