diff seqtk_nml.xml @ 0:e1867440ed36 draft

planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_nml.xml	Tue Sep 19 16:37:42 2017 -0400
@@ -0,0 +1,113 @@
+<tool id="seqtk_nml_sample" name="seqTK Sample NML" version="1.0.0">
+  <description>Runs seqTK sample if raw coverage is above user defined threshold </description>
+  <requirements>
+    <requirement type="package" version="1.2">seqtk</requirement>
+    <requirement type="package" version="1.6.924">perl-bioperl</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Unknown error has occured"/>
+  </stdio>
+  <command>
+		perl  $__tool_directory__/seqtk_nml.pl --ref $fastar 
+
+		#if $single_or_paired.type == "single"
+			--type single
+ 			--forward $input_se
+ 			--cov $coverage 
+			--out_forward $output
+			--log $log
+		#elif $single_or_paired.type == "paired"
+	        --type paired
+          	--forward $single_or_paired.forward_pe 
+		--reverse $single_or_paired.reverse_pe
+          	--cov $coverage 
+		--out_forward $output 
+		--out_reverse $output_rev
+		--log $log
+        #else
+            collection
+            $single_or_paired.fastq_collection.forward $single_or_paired.fastq_collection.reverse
+            $coverage $output_collection.forward $output_collection.reverse
+        #end if
+
+  </command>
+  <inputs>
+    <conditional name="single_or_paired">
+      <param name="type" type="select" label="Read type">
+	<option value="single">Single-end</option>
+        <option value="paired">Paired-end</option>
+        <option value="collection">Collection Paired-end</option>
+      </param>
+      <when value="single">
+	<param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
+      </when>
+      <when value="paired">
+	<param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
+        <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
+      </when>
+      <when value="collection">
+        <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" />
+      </when>
+    </conditional>
+    <param name="fastar" type="data" label="Fasta Reference File" format="fasta" />
+    <param name="coverage" type="integer" label="Desired Coverage" value="50" />
+  </inputs>
+  <outputs>
+    <data format="fastqsanger" name="output" label="SubSampled Fastq" >
+      <filter>single_or_paired['type']!="collection"</filter>
+    </data>
+    <data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse">
+      <filter>single_or_paired['type']=="paired"</filter>
+    </data>
+    <collection name="output_collection" type="paired" label="SubSampled Fastqs">
+      <data name="forward" format="fastqsanger"/>
+      <data name="reverse" format="fastqsanger"/>
+      <filter>single_or_paired['type']=="collection"</filter>
+    </collection>
+    <data format="txt" name="log" label="Log file"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="type" value="paired" />
+      <param name="forward_pe" value="inputforward.fastq" />
+      <param name="reverse_pe" value="inputreverse.fastq" />
+      <param name="fastar" value="testref.fasta"/>
+      <param name="coverage" value="50" />
+      <output name="output" file="outputforward.fastq" />
+      <output name="output_rev" file="outputreverse.fastq" />
+      <output name="log" file="lognosample.log" />
+    </test>
+    <test>
+      <param name="type" value="paired" />
+      <param name="forward_pe" value="inputforward.fastq" />
+      <param name="reverse_pe" value="inputreverse.fastq" />
+      <param name="fastar" value="testref.fasta"/>
+      <param name="coverage" value="25" />
+      <output name="output" file="outputdownsamepleforward.fastq" />
+      <output name="output_rev" file="outputdownsameplereverse.fastq" />
+      <output name="log" file="logdownsample.log" />
+    </test>
+  </tests>
+  <help>
+What it does
+============
+
+Calculates raw coverage. If the raw coverage is greater than desired coverage, runs seqTK sample to generate downsampled reads. 
+
+
+Usage
+=====
+
+**Parameters**
+	- Fastq reads (single end, paired end, or paired end collection)
+	- Fasta reference file
+
+**Options**
+	- Desired coverage (50)
+  </help>
+  <citations>
+    <citation type="doi">doi.org/10.1371/journal.pone.0163962</citation>
+  </citations>
+</tool>
+