diff pe_histogram.xml @ 0:2f6c7f82ad4a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pe_histogram.xml	Mon Jun 20 13:02:17 2016 -0400
@@ -0,0 +1,81 @@
+<tool id="pe_histogram" name="Paired-end histogram" version="1.0.0">
+    <description>of insert size frequency</description>
+    <requirements>
+        <requirement type="package" version="8.0.45">java-jdk</requirement>
+    </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range=":-1" />
+        <exit_code range="1:" />
+        <!-- Check stderr in case the return code has not been set -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+    <command>
+        <![CDATA[
+            ln -s "${input_bam}" "localbam.bam" &&
+            ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" &&
+            java -jar $__tool_directory__/PEHistogram.jar
+            -B "localbam.bam"
+            -I "localbam.bam.bai"
+            #if str($lower_limit) != '':
+                -l $lower_limit
+            #end if
+            #if str($upper_limit) != '':
+                -u $upper_limit
+            #end if
+            -p "$output1"
+            -t "$output2" 1>/dev/null
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="BAM file" />
+        <param name="lower_limit" type="integer" value="" optional="True" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/>
+        <param name="upper_limit" type="integer" value="" optional="True" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." />
+    </inputs>
+    <outputs>
+        <data name="output1" format="png" />
+        <data name="output2" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_bam" value="input.bam" ftype="bam" />
+            <output name="output1" file="output1.png" ftype="png" compare="sim_size" />
+            <output name="output2" file="output1.tabular" ftype="tabular" compare="contains" />
+        </test>
+        <test>
+            <param name="input_bam" value="input.bam" ftype="bam" />
+            <param name="lower_limit" value="200" />
+            <param name="upper_limit" value="300" />
+            <output name="output1" file="output2.png" ftype="png" compare="sim_size" />
+            <output name="output2" file="output2.tabular" ftype="tabular" compare="contains" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Produces an insert size histogram and basic statistics for a paired-end BAM file.  Two outputs are produced:
+
+- a png image consisting of the histogram of the insert size frequency
+- a tabular file containing the alignment statistics
+
+-----
+
+**Options**
+
+* **Lower bp limit** - the lower bp limit on insert size for calculating the histogram.
+* **Upper bp limit** - the upper bp limit on insert size for calculating the histogram.
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{None,
+            author = {Lai, William},
+            title = {None},
+            year = {None},
+            eprint = {None},
+            url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
+        }</citation>
+    </citations>
+</tool>