diff clipping_profile.xml @ 3:71ed55a3515a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83

--- a/clipping_profile.xml	Thu Jul 18 11:01:08 2013 -0500
+++ b/clipping_profile.xml	Tue Mar 14 10:22:57 2017 -0400
@@ -1,54 +1,85 @@
-<tool id="clipping_profile" name="Clipping Profile">
-	<description>
-	 estimates clipping profile of RNA-seq reads from BAM or SAM file
-	</description>
-	<requirements>
-		<requirement type="package" version="2.15.1">R</requirement>
-		<requirement type="package" version="2.3.7">rseqc</requirement>
-	</requirements>
-	<command>
-		clipping_profile.py -i $input -o output
-	</command>
-	<inputs>
-		<param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
-	</inputs>
-	<outputs>
-		<data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
-		<data format="r" name="outputr" from_work_dir="output.clipping_profile.r" />
-		<data format="pdf" name="outputpdf" from_work_dir="clipping_profile.pdf" />
-	</outputs>
-	<tests>
-		<test>
-			<param name="input" value="Pairend_StrandSpecific_51mer_Human_hg19.bam" />
-			<output name="outputxls" file="clipprofout.clipping_profile.xls" />
-			<output name="outputr" file="clipprofout.clipping_profile.r" />
-			<output name="outputpdf" file="clipping_profile.pdf" />
-		</test>
-	</tests>
-	<help>
-.. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
+<tool id="rseqc_clipping_profile" name="Clipping Profile" version="@WRAPPER_VERSION@">
+    <description>
+     estimates clipping profile of RNA-seq reads from BAM or SAM file
+    </description>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[clipping_profile.py --version]]></version_command>
+
+    <command><![CDATA[
+        clipping_profile.py -i '${input}' -o output -q ${mapq} -s "${layout}"
+        ]]>
+    </command>
+
+    <inputs>
+        <expand macro="bam_param" />
+        <expand macro="mapq_param" />
+        <expand macro="layout_param" />
+        <expand macro="rscript_output_param" />
+    </inputs>
 
------
+    <outputs>
+        <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" />
+        <expand macro="xls_output_data" filename="output.clipping_profile.xls" />
+        <expand macro="rscript_output_data" filename="output.clipping_profile.r" />
+    </outputs>
 
-About RSeQC
-+++++++++++
+    <tests>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
+            <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
+            <output name="outputxls" file="output.clipping_profile.xls" />
+        </test>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
+            <param name="rscript_output" value="true" />
+            <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
+            <output name="outputxls" file="output.clipping_profile.xls" />
+            <output name="outputr" file="output.clipping_profile.r" />
+        </test>
+    </tests>
 
-The RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq specific modules” investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
+    <help><![CDATA[
+clipping_profile.py
++++++++++++++++++++
 
-The RSeQC package is licensed under the GNU GPL v3 license.
+This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
+Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
+(This means your reads aligner should support clipped mapping).
 
 Inputs
 ++++++++++++++
 
 Input BAM/SAM file
-	Alignment file in BAM/SAM format.
+    Alignment file in BAM/SAM format.
 
+Minimum mapping quality
+    Minimum mapping quality for an alignment to be considered as "uniquely
+    mapped". default=30
+
+Sequencing layout
+    Denotes whether the sequecing was single-end (SE) or paired-end (PE).
 
 Sample Output
 ++++++++++++++
 
-.. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/clipping_good.png
+.. image:: $PATH_TO_IMAGES/clipping_good.png
+   :height: 600 px
+   :width: 600 px
+   :scale: 80 %
 
+@ABOUT@
 
-	</help>
-</tool>
\ No newline at end of file
+]]>
+    </help>
+
+    <expand macro="citations" />
+
+</tool>