# HG changeset patch
# User Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
# Date 1445012373 -3600
# Node ID b26c8f3b5aa65522a3d122bc23bb99eefddb8f77
# Parent  fb64b970da25fdfa5b07d6949d86f3ea9a844350
Use latest version of riboplot from PyPI (0.2.1)

diff -r fb64b970da25 -r b26c8f3b5aa6 README.rst
--- a/README.rst	Fri Sep 11 10:19:58 2015 +0100
+++ b/README.rst	Fri Oct 16 17:19:33 2015 +0100
@@ -14,7 +14,7 @@
 
 Free software: GPL license
 
-Documentation: https://riboplot.readthedocs.org
+Documentation: http://pythonhosted.org/riboplot
 
 Repository: https://github.com/vimalkumarvelayudhan/riboplot
 
diff -r fb64b970da25 -r b26c8f3b5aa6 ribocount.xml
--- a/ribocount.xml	Fri Sep 11 10:19:58 2015 +0100
+++ b/ribocount.xml	Fri Oct 16 17:19:33 2015 +0100
@@ -1,8 +1,8 @@
-<tool id="ribocount" name="ribocount" version="0.1.0">
+<tool id="ribocount" name="ribocount" version="0.2.0">
     <description>Get read counts for all transcripts in an alignment (BAM)
     </description>
     <requirements>
-        <requirement type="package" version="0.1.1">riboplot</requirement>
+        <requirement type="package" version="0.2.1">riboplot</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:"  level="fatal" description="Error" />
@@ -12,6 +12,11 @@
     --transcriptome_fasta "${transcriptome_fasta}"
     --read_length "${read_length}"
     --read_offset "${read_offset}"
+    #if (str($region_select) == 'five_prime'):
+    --count_five
+    #elif (str($region_select) == 'three_prime'):
+    --count_three
+    #end if
     --html_file "${html_file}"
     --output_path "${html_file.files_path}"
     ## --debug
@@ -19,11 +24,18 @@
     <inputs>
         <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/>
         <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/>
-        <param name="read_length" type="integer" label="Read length to consider" value="28"/>
+        <param name="read_length" type="integer" label="Read length to consider" value="28" help="If specified, only reads of this length will be considered.
+            A read length of 0 will output counts for all reads"/>
         <param name="read_offset" type="integer" label="Offset" value="0"/>
+        <param name="region_select" type="select" label="Which read counts to output?"
+            help="Output read counts for the entire transcript or restrict read counts to the region 5' or 3' of the longest ORF">
+            <option value="all_reads">All reads</option>
+            <option value="five_prime">5' of the longest ORF</option>
+            <option value="three_prime">3' of the longest ORF</option>
+        </param>
     </inputs>
     <outputs>
-        <data format="html" name="html_file" label="ribocount (HTML report)"/>
+        <data format="html" name="html_file" label="ribocount on ${ribo_file.name} ($region_select.value_label)"/>
     </outputs>
     <help>
 **RiboCount**
@@ -54,6 +66,11 @@
 
    If this option is provided, this offset is added to the read alignment positions.
 
+5. Restrict read counts
+
+   Choose whether to output read counts for the entire transcript or restrict read counts to the 5' or 3' region of the longest ORF.
+   Default start (ATG) and stop codons ('TAG', 'TGA', 'TAA') are used to identify the longest ORF in 3 frames.
+
 ----
 
 **Output**
diff -r fb64b970da25 -r b26c8f3b5aa6 riboplot.xml
--- a/riboplot.xml	Fri Sep 11 10:19:58 2015 +0100
+++ b/riboplot.xml	Fri Oct 16 17:19:33 2015 +0100
@@ -1,8 +1,8 @@
-<tool id="riboplot" name="riboplot" version="0.1.0">
+<tool id="riboplot" name="riboplot" version="0.2.0">
     <description>Plot and output read counts for a single transcript in an alignment (BAM)
     </description>
     <requirements>
-        <requirement type="package" version="0.1.1">riboplot</requirement>
+        <requirement type="package" version="0.2.1">riboplot</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:"  level="fatal" description="Error" />
@@ -78,7 +78,7 @@
 
    If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage.
 
-5. Read lengths to consider [Optional] (Integer - 0 or greater)
+5. Read lengths to consider [optional] (Integer - 0 or greater)
 
    If this option is provided, only Ribo-Seq data of the given length is considered.
 
diff -r fb64b970da25 -r b26c8f3b5aa6 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Sep 11 10:19:58 2015 +0100
+++ b/tool_dependencies.xml	Fri Oct 16 17:19:33 2015 +0100
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="riboplot" version="0.1.1">
+    <package name="riboplot" version="0.2.1">
         <install version="1.0">
             <actions>
-                <action type="setup_virtualenv">riboplot==0.1.1</action>
+                <action type="setup_virtualenv">riboplot==0.2.1</action>
                 <action type="set_environment">
                     <environment_variable action="set_to" name="RIBOPLOT_PATH">$INSTALL_DIR/venv/bin</environment_variable>
                 </action>