# HG changeset patch
# User Vimalkumar Velayudhan <vimal@biotechcoder.com>
# Date 1439369076 -3600
# Node ID 1901dcdc12ffe31288420d341afec67b2b895434
# Parent  8e1efafa627786a818d0a9c3a21c9fbeaf424eff
Move galaxy xml wrappers to top level

diff -r 8e1efafa6277 -r 1901dcdc12ff galaxy/ribocount.xml
--- a/galaxy/ribocount.xml	Wed Aug 12 09:27:45 2015 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-<tool id="ribocount" name="ribocount" version="0.1.0">
-    <description>Get read counts for all transcripts in an alignment (BAM)
-    </description>
-    <requirements>
-        <requirement type="package" version="0.8.3">pysam</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:"  level="fatal" description="Error" />
-    </stdio>
-    <command interpreter="python">../riboplot/ribocount.py
-    --ribo_file "${ribo_file}"
-    --transcriptome_fasta "${transcriptome_fasta}"
-    --read_length "${read_length}"
-    --read_offset "${read_offset}"
-    --html_file "${html_file}"
-    --output_path "${html_file.files_path}"
-    ## --debug
-    </command>
-    <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_offset" type="integer" label="Offset" value="0"/>
-    </inputs>
-    <outputs>
-        <data format="html" name="html_file" label="ribocount (HTML report)"/>
-    </outputs>
-    <help>
-    </help>
-</tool>
diff -r 8e1efafa6277 -r 1901dcdc12ff galaxy/riboplot.xml
--- a/galaxy/riboplot.xml	Wed Aug 12 09:27:45 2015 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-<tool id="riboplot" name="riboplot" version="0.1.0">
-    <description>Plot and output read counts for a single transcript in an alignment (BAM)
-    </description>
-    <requirements>
-        <requirement type="package" version="1.2.1">matplotlib</requirement>
-        <requirement type="package" version="0.8.3">pysam</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:"  level="fatal" description="Error" />
-    </stdio>
-    <command interpreter="python">../riboplot/riboplot.py
-    --ribo_file "${ribo_file}"
-    --transcriptome_fasta "${transcriptome_fasta}"
-    --transcript_name "${transcript_name}"
-    #if $rnacov.rnacov_select=="yes"
-        --rna_file "${rna_file}"
-    #end if
-    --read_length "${read_length}"
-    --read_offset "${read_offset}"
-    --html_file "${html_file}"
-    --output_path "${html_file.files_path}"
-    ## --debug
-    </command>
-    <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="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40">
-            <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
-            <validator type="empty_field" message="Field requires a value"/>
-            <sanitizer>
-                <valid>
-                    <add value="|"/>
-                </valid>
-            </sanitizer>
-        </param>
-        <conditional name="rnacov">
-            <param name="rnacov_select" type="select" label="Include RNA Coverage">
-                <option value="no">No</option>
-                <option value="yes">Yes</option>
-            </param>
-            <when value="yes">
-                <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/>
-            </when>
-            <when value="no" />
-        </conditional>
-        <param name="read_length" type="integer" label="Read length to consider" value="28"/>
-        <param name="read_offset" type="integer" label="Offset" value="0"/>
-    </inputs>
-    <outputs>
-        <data format="html" name="html_file" label="riboplot (HTML report)"/>
-    </outputs>
-    <help>
-    </help>
-</tool>
diff -r 8e1efafa6277 -r 1901dcdc12ff ribocount.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ribocount.xml	Wed Aug 12 09:44:36 2015 +0100
@@ -0,0 +1,30 @@
+<tool id="ribocount" name="ribocount" version="0.1.0">
+    <description>Get read counts for all transcripts in an alignment (BAM)
+    </description>
+    <requirements>
+        <requirement type="package" version="0.8.3">pysam</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"  level="fatal" description="Error" />
+    </stdio>
+    <command interpreter="python">riboplot/ribocount.py
+    --ribo_file "${ribo_file}"
+    --transcriptome_fasta "${transcriptome_fasta}"
+    --read_length "${read_length}"
+    --read_offset "${read_offset}"
+    --html_file "${html_file}"
+    --output_path "${html_file.files_path}"
+    ## --debug
+    </command>
+    <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_offset" type="integer" label="Offset" value="0"/>
+    </inputs>
+    <outputs>
+        <data format="html" name="html_file" label="ribocount (HTML report)"/>
+    </outputs>
+    <help>
+    </help>
+</tool>
diff -r 8e1efafa6277 -r 1901dcdc12ff riboplot.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/riboplot.xml	Wed Aug 12 09:44:36 2015 +0100
@@ -0,0 +1,54 @@
+<tool id="riboplot" name="riboplot" version="0.1.0">
+    <description>Plot and output read counts for a single transcript in an alignment (BAM)
+    </description>
+    <requirements>
+        <requirement type="package" version="1.2.1">matplotlib</requirement>
+        <requirement type="package" version="0.8.3">pysam</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"  level="fatal" description="Error" />
+    </stdio>
+    <command interpreter="python">riboplot/riboplot.py
+    --ribo_file "${ribo_file}"
+    --transcriptome_fasta "${transcriptome_fasta}"
+    --transcript_name "${transcript_name}"
+    #if $rnacov.rnacov_select=="yes"
+        --rna_file "${rna_file}"
+    #end if
+    --read_length "${read_length}"
+    --read_offset "${read_offset}"
+    --html_file "${html_file}"
+    --output_path "${html_file.files_path}"
+    ## --debug
+    </command>
+    <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="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40">
+            <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
+            <validator type="empty_field" message="Field requires a value"/>
+            <sanitizer>
+                <valid>
+                    <add value="|"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <conditional name="rnacov">
+            <param name="rnacov_select" type="select" label="Include RNA Coverage">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/>
+            </when>
+            <when value="no" />
+        </conditional>
+        <param name="read_length" type="integer" label="Read length to consider" value="28"/>
+        <param name="read_offset" type="integer" label="Offset" value="0"/>
+    </inputs>
+    <outputs>
+        <data format="html" name="html_file" label="riboplot (HTML report)"/>
+    </outputs>
+    <help>
+    </help>
+</tool>