diff small_rna_map.xml @ 0:1ad5d040f85f draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/small_rna_map.xml	Mon Jul 10 10:31:49 2017 -0400
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+<tool id="small_rna_map" name="small rna map" version="0.1.0">
+  <description></description>
+  <requirements>
+        <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
+        <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
+        <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement>
+        <requirement type="package" version="2.2.1=r3.3.1_0">r-ggplot2</requirement>
+        <requirement type="package" version="2.2.1=r3.3.1_0">r-gridextra</requirement>
+  </requirements>
+  <stdio>
+      <exit_code range="1:" level="fatal" description="Tool exception" />
+  </stdio>
+  <command detect_errors="exit_code"><![CDATA[
+      python '$__tool_directory__'/small_rna_map.py 
+      --input 
+      #for $file in $input
+            '$file'
+      #end for 
+      --output '$output_tab' &&
+      Rscript '$__tool_directory__'/small_rna_map.r --output_tab '$output_tab' --output_pdf '$output_pdf'
+  ]]></command>
+ <inputs>
+   <param name="input" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>                
+ </inputs>
+
+ <outputs>
+   <data format="tabular" name="output_tab" label="tabular file" />
+   <data format="pdf" name="output_pdf" label="PDF file" />
+</outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
+            <output file="output.tab" name="output_tab" />
+            <output file="output.pdf" name="output_pdf" />
+        </test>
+    </tests>
+
+
+<help>
+
+**What it does**
+
+Generate read count maps from alignment BAM files, using pysam and ggplot.
+In addition to the read counts (bars), median size and mean size of reads mapping at a given position are plotted in the graphs.	
+
+**Inputs**
+Bam alignment files. Be carreful to select Bam corresponding to alignments to the same reference
+
+**Output**
+A pdf file generated by the R package ggplot2
+
+</help>
+
+<citations>
+    <citation type="doi">10.1093/bioinformatics/btp352</citation>
+     <citation type="bibtex">@Book{,
+    author = {Hadley Wickham},
+    title = {ggplot2: Elegant Graphics for Data Analysis},
+    publisher = {Springer-Verlag New York},
+    year = {2009},
+    isbn = {978-0-387-98140-6},
+    url = {http://ggplot2.org},
+   }</citation>
+</citations>
+</tool>
+