diff splicetrap/splice_trap.xml @ 7:37a16ff93dd9 draft default tip

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/splicetrap/splice_trap.xml	Thu Oct 12 16:26:36 2017 -0400
@@ -0,0 +1,65 @@
+<tool id="splice_trap" name="SpliceTrap" version="1.0.0">
+    <description>A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing.
+    </description>
+    <requirements>
+        <requirement type="package" version="1.2.1.1">bowtie</requirement>
+    </requirements>
+    <command detect_errors="exit_code" interpreter="perl">
+    $__tool_directory__/SpliceTrap.pl -p 8 -l $__tool_directory__ -d hg38v3 -1 
+    #if $input_type_conditional.spliceTrap_input_type == "paired"
+            $input_type_conditional.input_1 -2 $input_type_conditional.input_2
+    #else
+            $input_type_conditional.input.forward -2 $input_type_conditional.input.reverse
+    #end if 
+    -s $read_size $output1 $output2
+    </command>
+    <inputs>
+        <conditional name="input_type_conditional">
+                <param name="spliceTrap_input_type" type="select" label="Input Type" help="Select between paired and paired collection">
+                        <option value="paired" selected="true">Paired</option>
+                        <option value="paired_collection">Paired Collection</option>
+                </param>
+                <when value="paired">
+                        <param format='fastq' name='input_1' type='data' label="FASTQ file, reverse reads" />
+                        <param format='fastq' name='input_2' type='data' label="FASTQ file, forward reads" />
+                </when>
+                <when value="paired_collection">
+                        <param format="fastq" name='input' type="data_collection" collection_type="paired" label="Select a paired collection" help="Specify paired dataset collection containing paired reads"/>
+                </when>
+        </conditional>
+        
+        <param name='read_size' type='integer' value='50' label="Read size"  />
+    </inputs>
+    <outputs>
+            <data format="txt" name="output1" />
+            <data format="txt" name="output2" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="input1.fastq"/>
+            <param name="input2" value="input2.fastq"/>
+            <output name="output1" file="output1.txt"/>
+            <output name="output2" file="output2.txt"/>
+        </test>
+        <test>
+            <param name="fastq_input">
+              <collection type="paired">
+                <element name="forward" value="input1.fastq" />
+                <element name="reverse" value="input2.fastq" />
+              </collection>
+            </param>
+            <param name="input_type" value="paired_collection" />
+            <output name="output1" file="output1.txt"/>
+            <output name="output2" file="output2.txt"/>
+        </test>
+    </tests>
+    <help>
+        **SpliceTrap**
+    </help>
+    <citations>
+        <citation type="bibtex">
+            http://rulai.cshl.edu/splicetrap
+        </citation>
+    </citations>
+</tool>
+