# HG changeset patch
# User drosofff
# Date 1460988548 14400
# Node ID ca3845fb0b3169a1c5513566ae1114c7c26eba5c
# Parent  b996480cd604701f39e60f728376602d4de52a06
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09

diff -r b996480cd604 -r ca3845fb0b31 sRbowtieParser.xml
--- a/sRbowtieParser.xml	Wed May 27 17:19:15 2015 -0400
+++ b/sRbowtieParser.xml	Mon Apr 18 10:09:08 2016 -0400
@@ -1,14 +1,12 @@
-<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.1">
+<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.6">
   <description></description>
   <requirements>
 	<requirement type="package" version="0.12.7">bowtie</requirement>
-        <requirement type="package" version="0.1.18">samtools</requirement>
         <requirement type="package" version="0.7.7">pysam</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
-        <requirement type="package" version="0.14">scipy</requirement>
  </requirements>
-<command interpreter="python">
-        sRbowtieParser.py 
+<command>
+        python $__tool_directory__/sRbowtieParser.py
 	          #if $refGenomeSource.genomeSource == "history":
                     --IndexSource $refGenomeSource.ownFile
          	    --ExtractDirective fastaSource
@@ -29,7 +27,7 @@
                   #end for
                   --alignmentLabel          
                   #for $i in $refGenomeSource.input_list
-                    "$i.name"
+                    "$i.element_identifier"
                   #end for
 
 </command>
@@ -40,13 +38,13 @@
                <option value="history">Use one from the history</option>
            </param>
            <when value="indexed">
-               <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true">
+               <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true">
                   <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
                </param>
            </when>
            <when value="history">
                 <param name="ownFile" type="data" format="fasta"  label="Select the fasta reference" />
-	        <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/>
+	        <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true"/>
            </when>
        </conditional>  <!-- refGenomeSource -->
        <param name="polarity" type="select" label="how to count sense and antisense reads">
diff -r b996480cd604 -r ca3845fb0b31 smRtools.py
--- a/smRtools.py	Wed May 27 17:19:15 2015 -0400
+++ b/smRtools.py	Mon Apr 18 10:09:08 2016 -0400
@@ -4,7 +4,8 @@
 import sys, subprocess
 from collections import defaultdict
 from numpy import mean, median, std
-from scipy import stats
+##Disable scipy import temporarily, as no working scipy on toolshed.
+##from scipy import stats
 
 def get_fasta (index="/home/galaxy/galaxy-dist/bowtie/5.37_Dmel/5.37_Dmel"):
   '''This function will return a dictionary containing fasta identifiers as keys and the
@@ -273,6 +274,8 @@
 
   def correlation_mapper (self, reference, window_size):
     '''to map correlation with a sliding window 26-2-2013'''
+    from scipy import stats
+
     if window_size > self.size:
       return []
     F=open(reference, "r")
diff -r b996480cd604 -r ca3845fb0b31 smRtools.pyc
Binary file smRtools.pyc has changed
diff -r b996480cd604 -r ca3845fb0b31 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed May 27 17:19:15 2015 -0400
+++ b/tool_dependencies.xml	Mon Apr 18 10:09:08 2016 -0400
@@ -3,16 +3,10 @@
   <package name="bowtie" version="0.12.7">
       <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="samtools" version="0.1.18">
-      <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
     <package name="pysam" version="0.7.7">
-      <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="0a5141bdf9d0" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="numpy" version="1.9">
-        <repository changeset_revision="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="scipy" version="0.14">
-        <repository changeset_revision="d470054f3a5d" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c8f7a7d73466" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>