diff small_rna_maps.xml @ 0:6d48150495e3 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/small_rna_maps.xml	Mon Jul 24 06:28:45 2017 -0400
@@ -0,0 +1,129 @@
+<tool id="small_rna_maps" name="small_rna_maps" version="0.9.0">
+  <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="0.6_28=r3.3.1_0">r-latticeextra</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[
+      #for $file in $input
+          samtools index '$file' &&
+      #end for
+      python '$__tool_directory__'/small_rna_maps.py 
+      --input 
+      #for $file in $input
+           '$file'
+      #end for
+          --sample_name
+      #for $sample in $input
+          '$sample.name'
+      #end for
+      #if $extra_plot == 'Sizes':
+          --sizes '$output_sizes'
+      #end if
+      --output '$output_tab' &&
+       Rscript '$__tool_directory__'/small_rna_maps.r --output_tab '$output_tab' 
+               --output_pdf '$output_pdf'
+      #if $extra_plot != 'Sizes':
+          --extra_plot '$extra_plot'
+      #else
+          --sizes $output_sizes
+      #end if
+  ]]></command>
+ <inputs>
+   <param name="input" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> 
+   <param name="extra_plot" type="select" label="select the type of extra plot in addition to read map">
+       <option value="Coverage">Coverage</option> 
+       <option value="Mean">Mean Sizes</option> 
+       <option value="Median">Median Sizes</option>
+       <option value="Sizes">Size Distributions</option>
+    </param>
+ </inputs>
+
+ <outputs>
+   <data format="tabular" name="output_tab" label="Map dataframe" />
+   <data format="tabular" name="output_sizes" label="Size dataframe" >
+       <filter>extra_plot == "Sizes"</filter>
+   </data>
+   <data format="pdf" name="output_pdf" label="PDF file" />
+
+</outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
+            <param name="extra_plot" value="Mean" />
+            <output file="output.tab" name="output_tab" />
+            <output file="mean.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="input" value="input1.bam,input1.bam" ftype="bam"/>
+            <param name="extra_plot" value="Mean" />
+            <output file="doubled.tab" name="output_tab" />
+            <output file="doubled_mean.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
+            <param name="extra_plot" value="Median" />
+            <output file="output.tab" name="output_tab" />
+            <output file="median.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
+            <param name="extra_plot" value="Coverage" />
+            <output file="output.tab" name="output_tab" />
+            <output file="coverage.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
+            <param name="extra_plot" value="Sizes" />
+            <output file="output.tab" name="output_tab" />
+            <output file="sizes.tab" name="output_sizes" />
+            <output file="sizes.pdf" name="output_pdf" />
+        </test>
+    </tests>
+
+
+<help>
+
+**What it does**
+
+Generate read count maps from alignment BAM files, using pysam and lattice.
+
+In addition to the read counts (lower graphs), median size, mean size and coverage depth of reads(lower graphs) mapping at a given position are plotted.	
+
+**Inputs**
+
+bam alignment files that *must* be
+
+  - single-read
+  - sorted
+  - mapping to the same reference
+
+**Output**
+
+A pdf file generated by the R package lattice
+
+One or two dataframes used to plot data
+
+</help>
+
+<citations>
+    <citation type="doi">10.1093/bioinformatics/btp352</citation>
+     <citation type="bibtex">@Book{,
+    title = {Lattice: Multivariate Data Visualization with R},
+    author = {Deepayan Sarkar},
+    publisher = {Springer},
+    address = {New York},
+    year = {2008},
+    note = {ISBN 978-0-387-75968-5},
+    url = {http://lmdvr.r-forge.r-project.org},
+  }</citation>
+</citations>
+</tool>
+