Mercurial > repos > artbio > small_rna_map

diff small_rna_map.xml @ 3:2e0dc6032a98 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
author artbio
date Tue, 18 Jul 2017 13:34:36 -0400
parents 7feee0446c5c
children 6ff925458e05
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line diff
--- a/small_rna_map.xml	Wed Jul 12 13:40:36 2017 -0400
+++ b/small_rna_map.xml	Tue Jul 18 13:34:36 2017 -0400
@@ -5,6 +5,7 @@
         <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="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>
@@ -15,12 +16,25 @@
       --input 
       #for $file in $input
             '$file'
-      #end for 
+      #end for
+      --sample_name
+      #for $sample in $input
+          '$sample.name'
+      #end for
       --output '$output_tab' &&
-      Rscript '$__tool_directory__'/small_rna_map.r --output_tab '$output_tab' --output_pdf '$output_pdf'
+      #if $R_method=='lattice':
+          Rscript '$__tool_directory__'/lattice_small_rna_map.r --output_tab '$output_tab' --output_pdf '$output_pdf'
+      #else:
+          Rscript '$__tool_directory__'/small_rna_map.r --output_tab '$output_tab' --output_pdf '$output_pdf'
+      #end if
   ]]></command>
  <inputs>
-   <param name="input" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>                
+   <param name="input" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>     
+    <param help="Select the R package to produce graphics" label="lattice or ggplot" name="R_method" type="select">
+                <option selected="True" value="lattice">lattice</option>
+                <option value="ggplot">ggplot</option>
+            </param>
+              
  </inputs>
 
  <outputs>
@@ -30,10 +44,29 @@
 
     <tests>
         <test>
-            <param name="input" value="input1.bam,input2.bam,input3.bam,input4.bam" ftype="bam"/>
+            <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
+            <param name="R_method" value="lattice" />
+            <output file="output.tab" name="output_tab" />
+            <output file="output_lattice.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="input" value="input1.bam,input1.bam" ftype="bam"/>
+            <param name="R_method" value="lattice" />
+            <output file="output_doubled.tab" name="output_tab" />
+            <output file="output_lattice_doubled.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
+            <param name="R_method" value="ggplot" />
             <output file="output.tab" name="output_tab" />
             <output file="output.pdf" name="output_pdf" />
         </test>
+        <test>
+            <param name="input" value="input1.bam,input1.bam" ftype="bam"/>
+            <param name="R_method" value="ggplot" />
+            <output file="output_doubled.tab" name="output_tab" />
+            <output file="output_doubled.pdf" name="output_pdf" />
+        </test>
     </tests>