# HG changeset patch
# User drosofff
# Date 1497174989 14400
# Node ID 74394e39ad22b9e7054af8d1e6c7f1415d5ea51d
# Parent  933475df0fd2912103ec97a5672cc290ad27b5fa
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f

diff -r 933475df0fd2 -r 74394e39ad22 MirParser.py
--- a/MirParser.py	Wed Oct 21 11:25:01 2015 -0400
+++ b/MirParser.py	Sun Jun 11 05:56:29 2017 -0400
@@ -8,7 +8,7 @@
 import sys
 import subprocess
 
-from smRtools import *
+from smRtools import HandleSmRNAwindows
 
 IndexSource = sys.argv[1]
 ExtractionDirective = sys.argv[2]
diff -r 933475df0fd2 -r 74394e39ad22 MirParser.xml
--- a/MirParser.xml	Wed Oct 21 11:25:01 2015 -0400
+++ b/MirParser.xml	Sun Jun 11 05:56:29 2017 -0400
@@ -1,40 +1,38 @@
-<tool id="MirParser" name="Parse miRNAs" version="0.9.4">
+<tool id="MirParser" name="Parse miRNAs" version="0.9.6">
     <description>from aligment files</description>
     <requirements>
-        <requirement type="package" version="0.12.7">bowtie</requirement>
-        <requirement type="package" version="0.7.7">pysam</requirement>
-        <requirement type="package" version="1.9">numpy</requirement>
-        <requirement type="package" version="3.1.2">R</requirement>
-        <requirement type="package" version="2.14">biocbasics</requirement>
-        <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="package" version="1.1.2">bowtie</requirement>
+        <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="0.20_33=r3.3.1_0">r-lattice</requirement>
     </requirements>
-    <command interpreter="python">
-        MirParser.py 
-	          #if $refGenomeSource.genomeSource == "history":
-                    $refGenomeSource.ownFile ## index source sys.arg[1]
-         	    --do_not_extract_index  ## sys.argv[2]
-          	  #else:
-		    #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
-		    $reference   ## sys.argv[1]
+    <command><![CDATA[
+        python '$__tool_directory__'/MirParser.py
+	    #if $refGenomeSource.genomeSource == "history":
+            '$refGenomeSource.ownFile' ## index source sys.arg[1]
+            --do_not_extract_index  ## sys.argv[2]
+        #else:
+		    #silent reference = filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
+		    '$reference'   ## sys.argv[1]
 		    --extract_index  ## sys.argv[2]
-          	  #end if
-		  $output1 ## for pre-mirs  ## sys.argv[3]
-		  $output2 ## for mature mirs  ## sys.argv[4]
-		  $GFF3    ## sys.argv[5]
-		  #if $plotting.plottingOption == "yes":
-		    $lattice_dataframe   ## sys.argv[6]
-		    $plotCode   ## sys.argv[7]
-		    $latticePDF ## sys.argv[8]
-		  #else:
+        #end if
+		'$output1' ## for pre-mirs  ## sys.argv[3]
+		'$output2' ## for mature mirs  ## sys.argv[4]
+		'$GFF3'    ## sys.argv[5]
+		#if $plotting.plottingOption == "yes":
+		    '$lattice_dataframe'   ## sys.argv[6]
+		    '$plotCode'   ## sys.argv[7]
+		    '$latticePDF' ## sys.argv[8]
+		#else:
 		    "dummy_dataframe_path"   ## sys.argv[6]
-                    "dummy_plotCode"   ## sys.argv[7]
+            "dummy_plotCode"   ## sys.argv[7]
 		    "dummy_latticePDF" ## sys.argv[8]
-		  #end if
-		  #for $i in $refGenomeSource.input_list
-    		    $i $i.ext "$i.name" ## sys.argv[9,10,11] modulo 3
-		  #end for
-                  #silent plottingoption = $plotting.plottingOption
-</command>
+		#end if
+		#for $i in $refGenomeSource.input_list
+    	    '$i' '$i.ext' "$i.name" ## sys.argv[9,10,11] modulo 3
+		#end for
+        #silent plottingoption = $plotting.plottingOption
+    ]]></command>
     <inputs>
         <conditional name="refGenomeSource">
             <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">
diff -r 933475df0fd2 -r 74394e39ad22 smRtools.py
--- a/smRtools.py	Wed Oct 21 11:25:01 2015 -0400
+++ b/smRtools.py	Sun Jun 11 05:56:29 2017 -0400
@@ -142,26 +142,6 @@
           self.alignedReads += 1
       F.close()
       return self.instanceDict
-#    elif self.alignmentFileFormat == "sam":
-#      F = open (self.alignmentFile, "r")
-#      dict = {"0":"+", "16":"-"}
-#      for line in F:
-#        if line[0]=='@':
-#            continue
-#        fields = line.split()
-#        if fields[2] == "*": continue
-#        polarity = dict[fields[1]]
-#        gene = fields[2]
-#        offset = int(fields[3])
-#        size = len (fields[9])
-#        if self.size_inf:
-#          if (size>=self.size_inf and size<= self.size_sup):
-#            self.instanceDict[gene].addread (polarity, offset, size)
-#            self.alignedReads += 1
-#       else:
-#          self.instanceDict[gene].addread (polarity, offset, size)
-#          self.alignedReads += 1
-#      F.close()
     elif self.alignmentFileFormat == "bam" or self.alignmentFileFormat == "sam":
       import pysam
       samfile = pysam.Samfile(self.alignmentFile)
@@ -184,22 +164,6 @@
           self.alignedReads += 1
       return self.instanceDict
 
-#  def size_histogram (self):
-#    size_dict={}
-#    size_dict['F']= defaultdict (int)
-#    size_dict['R']= defaultdict (int)
-#    size_dict['both'] = defaultdict (int)
-#    for item in self.instanceDict:
-#      buffer_dict_F = self.instanceDict[item].size_histogram()['F']
-#      buffer_dict_R = self.instanceDict[item].size_histogram()['R']
-#      for size in buffer_dict_F:
-#        size_dict['F'][size] += buffer_dict_F[size]
-#      for size in buffer_dict_R:
-#        size_dict['R'][size] -= buffer_dict_R[size]
-#    allSizeKeys = list (set (size_dict['F'].keys() + size_dict['R'].keys() ) )
-#    for size in allSizeKeys:
-#      size_dict['both'][size] = size_dict['F'][size] + size_dict['R'][size]
-#    return size_dict
   def size_histogram (self): # in HandleSmRNAwindows
     '''refactored on 7-9-2014 to debug size_histogram tool'''
     size_dict={}
@@ -361,24 +325,7 @@
     for offset in range (min(dicsize.keys()), max(dicsize.keys())+1):
       dicsize[size] = dicsize.get(size, 0) # to fill offsets with null values
     return dicsize
-    
-#  def size_histogram(self):
-#    norm=self.norm
-#    hist_dict={}
-#    hist_dict['F']={}
-#    hist_dict['R']={}
-#    for offset in self.readDict:
-#      for size in self.readDict[offset]:
-#        if offset < 0:
-#          hist_dict['R'][size] = hist_dict['R'].get(size, 0) - 1*norm
-#        else:
-#          hist_dict['F'][size] = hist_dict['F'].get(size, 0) + 1*norm
-#   ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate !    
-#    if not (hist_dict['F']) and (not hist_dict['R']):
-#      hist_dict['F'][21] = 0
-#      hist_dict['R'][21] = 0
-#   ##
-#    return hist_dict
+
 
   def size_histogram(self, minquery=None, maxquery=None): # in SmRNAwindow
     '''refactored on 7-9-2014 to debug size_histogram tool'''
@@ -480,7 +427,6 @@
       return ". | %s" % (freqDic["Trev"] / reverse_sum * 100)
     else:
       return "%s | %s" % (freqDic["Tfor"] / forward_sum * 100, freqDic["Trev"] / reverse_sum * 100)
-
     
   def readplot (self):
     norm=self.norm
diff -r 933475df0fd2 -r 74394e39ad22 smRtools.pyc
Binary file smRtools.pyc has changed
diff -r 933475df0fd2 -r 74394e39ad22 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Oct 21 11:25:01 2015 -0400
+++ b/tool_dependencies.xml	Sun Jun 11 05:56:29 2017 -0400
@@ -1,21 +1,18 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <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 name="bowtie" version="1.1.2">
+      <repository changeset_revision="8584a4574ab1" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="pysam" version="0.7.7">
-      <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="pysam" version="0.8.3">
+      <repository changeset_revision="7ac80143c68d" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="numpy" version="1.9">
-        <repository changeset_revision="816d3480b0b1" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="5f2b261ffc5b" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="R" version="3.1.2">
-        <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="biocbasics" version="2.14">
         <repository changeset_revision="d243626801e2" name="package_biocbasics_2_14" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="samtools" version="1.2">
-        <repository changeset_revision="192f00129358" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
 </tool_dependency>