diff tabular_to_fastq.xml @ 3:643018aa1435 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a

--- a/tabular_to_fastq.xml	Fri Dec 18 19:31:46 2015 -0500
+++ b/tabular_to_fastq.xml	Sat Sep 30 13:54:43 2017 -0400
@@ -1,45 +1,41 @@
-<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.0.0">
-  <description>converter</description>
-  <requirements>
-    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
-  </requirements>
-  <command interpreter="python">tabular_to_fastq.py '$input_file' '$output_file' '$identifier' '$sequence' '$quality'</command>
-  <inputs>
-    <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
-    <param name="identifier" label="Identifier column" type="data_column" data_ref="input_file" />
-    <param name="sequence" label="Sequence column" type="data_column" data_ref="input_file" />
-    <param name="quality" label="Quality column" type="data_column" data_ref="input_file" />
-  </inputs>
-  <outputs>
-    <data name="output_file" format="fastq" />
-  </outputs>
-  <tests>
-    <!-- basic test -->
-    <test>
-      <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
-      <param name="identifier" value="1" />
-      <param name="sequence" value="2" />
-      <param name="quality" value="3" />
-      <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
-    </test>
-    <!-- color space test -->
-    <test>
-      <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
-      <param name="identifier" value="1" />
-      <param name="sequence" value="2" />
-      <param name="quality" value="3" />
-      <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
-    </test>
-  </tests>
-  <help>
+<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.1.1">
+    <description>converter</description>
+    <command><![CDATA[
+python '$__tool_directory__/tabular_to_fastq.py' '$input_file' '$output_file' '$identifier' '$sequence' '$quality'
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
+        <param name="identifier" type="data_column" data_ref="input_file" label="Identifier column" />
+        <param name="sequence" type="data_column" data_ref="input_file" label="Sequence column" />
+        <param name="quality" type="data_column" data_ref="input_file" label="Quality column" />
+    </inputs>
+    <outputs>
+        <data name="output_file" format="fastq" />
+    </outputs>
+    <tests>
+        <!-- basic test -->
+        <test>
+            <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
+            <param name="identifier" value="1" />
+            <param name="sequence" value="2" />
+            <param name="quality" value="3" />
+            <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
+        </test>
+        <!-- color space test -->
+        <test>
+            <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
+            <param name="identifier" value="1" />
+            <param name="sequence" value="2" />
+            <param name="quality" value="3" />
+            <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
-This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool. 
-
-  </help>
-  
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq281</citation>
-  </citations>
-  
+This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btq281</citation>
+    </citations>
 </tool>