# HG changeset patch
# User mvdbeek
# Date 1427648877 14400
# Node ID eee9701a7491c3c1269f8f6c43ed3c7a4a9f4110
# Parent  9af9983dcd02e9d7e9fceced392efbb8b8679a12
Uploaded

diff -r 9af9983dcd02 -r eee9701a7491 readmap.xml
--- a/readmap.xml	Mon Nov 03 10:28:40 2014 -0500
+++ b/readmap.xml	Sun Mar 29 13:07:57 2015 -0400
@@ -6,8 +6,9 @@
         <requirement type="package" version="0.7.7">pysam</requirement>
         <requirement type="package" version="2.14">biocbasics</requirement>
         <requirement type="package" version="3.0.3">R</requirement>
+        <requirement type="package" version="1.9">numpy</requirement>
+        <requirement type="package" version="0.14">scipy</requirement>
   </requirements>
-  <parallelism method="basic"></parallelism>
 <command interpreter="python">
         readmap.py 
 	          #if $refGenomeSource.genomeSource == "history":
@@ -258,23 +259,27 @@
     :width: 500
 
 </help>
-
+  <tests>
   <test>
       <param name="genomeSource" value="history" />
       <param name="ownFile" value ="transposons.fasta" ftype="fasta" />
-      <param name="input" value="sample1.srbowtie_out, sample2.srbowtie_out, sample3.srbowtie_out" ftype="tabular" />
-      <param name="norm" value="1,1,1" />
+      <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/>
+      <param name="series_0|norm" value="1" />
+      <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/>
+      <param name="series_1|norm" value="1" />
+      <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/>
+      <param name="series_2|norm" value="1" />
       <param name="minquery" value="20" />
       <param name="maxquery" value="30" />
       <param name="title" value="Readmaps and size distributions" />
       <param name="xlabel" value="Coordinates/read size" />
       <param name="ylabel" value="Number of reads" />
       <param name="rows_per_page" value="8" />
-      <output name="readmap_dataframe" ftype="tabular" value="Readmap_dataframe.tab" />
-      <output name="size_distribution_dataframe" ftype="tabular" value="Size_distribution_dataframe.tab" />
-      <output name="readmap_PDF" ftype="pdf" value="Readmaps.pdf" />
-      <output name="size_PDF" ftype="pdf" value="Size_distribution.pdf" />
-      <output name="combi_PDF" ftype="pdf" value="Size_distribution_and_Readmaps.pdf" />
+      <output name="readmap_dataframe" ftype="tabular" file="Readmap_dataframe.tab" />
+      <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" />
+      <output name="readmap_PDF" ftype="pdf" file="Readmaps.pdf" />
+      <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" />
+      <output name="combi_PDF" ftype="pdf" file="Size_distribution_and_Readmaps.pdf" />
   </test>
-
+  </tests>
 </tool>
diff -r 9af9983dcd02 -r eee9701a7491 runme.R
--- a/runme.R	Mon Nov 03 10:28:40 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-bioclite = "http://bioconductor.org/biocLite.R"
-install.packages(c("lattice","latticeExtra"),dependencies=T,repos=http://cran.us.r-project.org)
-source(bioclite)
-installme=c(lattice,latticeExtra)
-biocLite()
-biocLite(installme)
-quit(save="no")
-
diff -r 9af9983dcd02 -r eee9701a7491 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 03 10:28:40 2014 -0500
+++ b/tool_dependencies.xml	Sun Mar 29 13:07:57 2015 -0400
@@ -1,22 +1,22 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="bowtie" version="0.12.7">
-      <repository changeset_revision="f54826948b0b" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="bowtie" version="0.12.7">
+      <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.18">
       <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="pysam" version="0.7.7">
-      <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="R" version="3.0.3">
-      <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="biocbasics" version="2.14">
       <install version="1.0">
           <actions>
               <action type="set_environment_for_install">
-                  <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                  <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                       <package name="R" version="3.0.3" />
                     </repository>
                 </action>
@@ -31,6 +31,12 @@
                 <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
             </actions>
         </install>
+    <package name="numpy" version="1.9">
+        <repository name="package_numpy_1_9" owner="iuc" prior_installation_required="True" />
+    </package>
+    <package name="scipy" version="0.14">
+        <repository name="package_scipy_0_14" owner="iuc" prior_installation_required="True" />
+    </package>
         <readme>Installs some basic bioc packages for the lattice wrapper and grid + gridExtra for managing lattice panels
         It's clunky but this is the most convenient way iuc could get anything installed into the package_r3
         Note we use cran at fred hutch since no fastest mirror thingy