# HG changeset patch
# User artbio
# Date 1500413752 14400
# Node ID 6ff925458e05ef4bf2ba4d113f5e3fbbfd380f45
# Parent  2e0dc6032a98f31921794dc41ab86a0cf57bc78a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit dcd643f146afe371d3e418aa91ddbaff6211a09a

diff -r 2e0dc6032a98 -r 6ff925458e05 lattice_small_rna_map.r
--- a/lattice_small_rna_map.r	Tue Jul 18 13:34:36 2017 -0400
+++ b/lattice_small_rna_map.r	Tue Jul 18 17:35:52 2017 -0400
@@ -34,7 +34,8 @@
     combineLimits(xyplot(Nbr_reads~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
     data=df,
     type='h',
-    scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.1), y=list(tick.number=4, rot=90, cex=0.7)),
+    lwd=1.5,
+    scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
     xlab=NULL, main=NULL, ylab=NULL,
     as.table=T,
     origin = 0,
@@ -51,7 +52,7 @@
     sizeplot = xyplot(Median~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
     data=df,
     type='p',
-    cex=0.5,
+    cex=0.35,
     pch=19,
     scales= list(relation="free", x=list(rot=0, cex=0, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
     xlab=NULL, main=NULL, ylab=NULL,
@@ -75,7 +76,7 @@
 
 ## GRAPHS
 
-if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=10} else {
+if (n_genes > 5) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=6} else {
                  rows_per_page= n_genes; page_height_simple = 2.5*n_genes; page_height_combi=page_height_simple*2 }
 if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/2} # to test
 
diff -r 2e0dc6032a98 -r 6ff925458e05 small_rna_map.xml
--- a/small_rna_map.xml	Tue Jul 18 13:34:36 2017 -0400
+++ b/small_rna_map.xml	Tue Jul 18 17:35:52 2017 -0400
@@ -1,10 +1,9 @@
-<tool id="small_rna_map" name="small rna map" version="0.3.0">
+<tool id="small_rna_map" name="small rna map" version="0.4.0">
   <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="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>
@@ -22,19 +21,10 @@
           '$sample.name'
       #end for
       --output '$output_tab' &&
-      #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 '$output_pdf'
-      #end if
+       Rscript '$__tool_directory__'/lattice_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"/>     
-    <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>
@@ -45,28 +35,14 @@
     <tests>
         <test>
             <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>
 
 
diff -r 2e0dc6032a98 -r 6ff925458e05 test-data/output_lattice.pdf
Binary file test-data/output_lattice.pdf has changed
diff -r 2e0dc6032a98 -r 6ff925458e05 test-data/output_lattice_doubled.pdf
Binary file test-data/output_lattice_doubled.pdf has changed