# HG changeset patch
# User Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
# Date 1445342705 -3600
# Node ID f40b0b26e7667dd79959072cf03e2b9e15eec01e

First commit

diff -r 000000000000 -r f40b0b26e766 RUST_metafootprints.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RUST_metafootprints.xml	Tue Oct 20 13:05:05 2015 +0100
@@ -0,0 +1,76 @@
+<tool id="rust_amino1" name="Metafootprint analysis" version="1">
+       <description>(Step 1)</description>
+    <requirements>
+        <requirement type="package" version="0.1.0">RUST</requirement>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+    </requirements>
+            <command> 
+                #if str( $metafootprint_type ) == "Nucleotide"
+                    python \${RUST_PATH}/RUST_nucleotide.py $input $alignment  $offset $include_lengths $html_file.files_path $html_file $output1
+                #end if
+                #if str( $metafootprint_type ) == "Codon"
+                    python \${RUST_PATH}/RUST_codon.py $input $alignment $offset $include_lengths $html_file.files_path $html_file $output1
+                #end if
+                #if str( $metafootprint_type ) == "Amino"
+                    python \${RUST_PATH}/RUST_amino.py $input $alignment $offset $include_lengths $html_file.files_path $html_file $output1
+                #end if                    
+                #if str( $metafootprint_type ) == "Dipeptide"
+                    python \${RUST_PATH}/RUST_dipeptide.py $input $alignment $offset $include_lengths $html_file.files_path $html_file $output1
+                #end if     
+                #if str( $metafootprint_type ) == "Tripeptide"
+                    python \${RUST_PATH}/RUST_tripeptide.py $input $alignment  $offset $include_lengths $html_file.files_path $html_file $output1
+                #end if
+                </command>
+
+   <inputs>
+     <param format="fasta" name="input" type="data" label="Transcriptome file" help="A fasta file whose transcripts are used to produce the metafootprint profile."/>
+     <param format="bam" name="alignment" type="data" label="Alignment file" help="The alignments of ribo-seq/mRNA-seq reads to the Transcriptome file. This should be a sorted bam file."/>
+     <param name="offset" value="15" type="integer" label="Nucleotide offset to A-site"/>
+     <param name="include_lengths" type="text"
+               label="Lengths of ribosome footprints
+             to be included"
+               help="Here you can specify the lengths of ribosome footprints to
+             be included (28:32 includes reads of length 28,29,30,31,32)."
+              value="28:32"/>
+     <param name="metafootprint_type" type="select" label="Metafootprint type" help="Sequence features that may influence read density">
+        <option value="Nucleotide">Nucleotide</option>
+        <option value="Codon">Codon</option>
+        <option value="Amino">Amino</option>
+        <option value="Dipeptide">Dipeptide</option>
+        <option value="Tripeptide">Tripeptide</option>
+      </param>
+      
+   </inputs>
+   <outputs>
+       <data format="csv" name="output1" label = "$tool.name [$metafootprint_type] on $on_string" />
+     <data format="html" name="html_file" label="$tool.name [$metafootprint_type png] on $on_string" >  
+     </data>
+   </outputs>
+ 
+
+ 
+   <help>
+**What it does**
+
+This tool produces a RUST metafootprint profile that reveals the influence of mRNA features such as codons/amino acids on the relative read density in the sample across the entire ribosome and nascent peptide region. The Kullback-Leibler divergence across these sites is also provided.
+
+------
+
+**Transcriptome file**
+
+By default the RUST analysis is carried out on the longest ORF in each transcript. Alternatively the user may provide alignments to the entire transcripts with information of both the translation initiation and termination sites. These are to be provided along side the name of each transcript in Transcriptome file. It must be in a tab delimited and in the following format ">transcript name{tab}initiation site coordinate{tab}termination site coordinate". 
+
+The alignments used to produce the RUST values start 120 nucleotides after the start codon and finish 60 nucleotides before the stop codon. Transcripts with ORF length less than 230 nucleotides and those whose reading frame is not divisible by three are ignored.
+
+------
+
+**Citation**
+
+Surveying the relative impact of mRNA features on local ribosome profiling read density in 28 datasets.
+Patrick O'Connor, Dmitry Andreev, Pavel Baranov
+bioRxiv doi: http://dx.doi.org/10.1101/018762
+
+
+   </help>
+ 
+</tool>
diff -r 000000000000 -r f40b0b26e766 footprint_codons.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/footprint_codons.xml	Tue Oct 20 13:05:05 2015 +0100
@@ -0,0 +1,45 @@
+
+<tool id="footprint_codon" name="Similarity of observed and expected profiles" version="1">
+    <description>(Step 3)</description>
+    <requirements>
+        <requirement type="package" version="0.1.0">RUST</requirement>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+    </requirements>
+   <command>python \${RUST_PATH}/footprint_codons.py $input $alignment $offset $include_lengths $observed_codon $output1 </command>
+   <inputs>
+     <param format="fasta" name="input" type="data" label="Transcriptome file" help="A fasta file whose transcripts are used to produce the metafootprint profile."/>
+     <param format="bam" name="alignment" type="data" label="Alignment file" help="The alignments of ribo-seq/mRNA-seq reads to the Transcriptome file. This should be a sorted bam file."/>
+     <param name="offset" value="17" type="integer" label="Nucleotide offset to A-site"/>
+     <param name="include_lengths" type="text"
+               label="Lengths of ribosome footprints
+             to be included"
+            help="Here you can specify the lengths of ribosome footprints to
+             be included (28:32 includes reads of length 28,29,30,31,32)."
+              value="28:32">
+<!--       <validator type="expression" message="Please input correct format">len(value.split(':')) == 2</validator> -->
+      </param>           
+     <param format="csv" name="observed_codon" type="data" label="Codon metafootprint" help="RUST codon metafootprint analysis">
+      </param>           
+   </inputs>
+   <outputs>
+     <data format="csv" name="output1" help="Contains prediction of ribosome profile for transcripts in Transcriptome file that fulfill certain criteria" />
+   </outputs>
+ 
+
+ 
+   <help>
+**What it does**
+
+Uses the observed codon RUST ratios of 12 sites (A-site-6 to A-site+5) to calculate alignment probabilities along the elongation region of each transcript. It then compares the similarity between the expected and observed ribosome profiles using both Spearman's and Pearson's correlation coefficients. This is returned in a csv file.
+
+------
+
+**Citation**
+
+Surveying the relative impact of mRNA features on local ribosome profiling read density in 28 datasets.
+Patrick O'Connor, Dmitry Andreev, Pavel Baranov
+bioRxiv doi: http://dx.doi.org/10.1101/018762
+
+   </help>
+ 
+</tool>
diff -r 000000000000 -r f40b0b26e766 observed_expected.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/observed_expected.xml	Tue Oct 20 13:05:05 2015 +0100
@@ -0,0 +1,58 @@
+
+<tool id="plot_RUST_profile" name="Plot transcripts predicted profiles" version="1">
+    <description>(Step 4)</description>
+    <requirements>
+        <requirement type="package" version="0.1.0">RUST</requirement>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+    </requirements>
+   <command>python \${RUST_PATH}/observed_expected.py $input $alignment $offset $include_lengths $observed_codon $transcript_name $html_file.files_path $html_file </command>
+   <inputs>
+       <param name="transcript_name" type="text" size="30"
+               label="Name of the transcript to be plotted"
+               help="Specific transcript to plot (Use of unique identifier is sufficient for example either '815891337' and 'NM_031946' for 'gi|815891337|ref|NM_031946.6|')">
+            <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
+            <validator type="empty_field" message="Field requires a value"/>
+            <sanitizer>
+                <valid>
+                    <add value="|"/>
+                </valid>
+            </sanitizer>
+        </param>
+        
+     <param format="fasta" name="input" type="data" label="Transcriptome file" help="A fasta file whose transcripts are used to produce the metafootprint profile."/>
+     <param format="bam" name="alignment" type="data" label="Alignment file" help="The alignments of ribo-seq/mRNA-seq reads to the Transcriptome file. This should be a sorted bam file."/>
+     <param name="offset" value="17" type="integer" label="Nucleotide offset to A-site"/>
+     <param name="include_lengths" type="text"
+               label="Lengths of ribosome footprints
+             to be included"
+               help="Here you can specify the lengths of ribosome footprints to
+             be included (28:32 includes reads of length 28,29,30,31,32)."
+              value="28:32">
+<!--       <validator type="expression" message="Please input with correct format">len(value.split(':')) == 2</validator> -->
+      </param>             
+     <param format="csv" name="observed_codon" type="data" label="Codon metafootprint" help="RUST codon metafootprint analysis"/>
+   </inputs>
+
+   <outputs>
+      <data format="html" name="html_file" label="$tool.name on $on_string" >  
+     </data>
+   </outputs>
+ 
+
+ 
+   <help>
+**What it does**
+
+Returns both the observed and and expected profiles for a transcript specified by the user in a csv file. A image of both profiles is provided. The data is provided for 120 nucleotides after the start codon and 60 nucleotides before the stop codon.
+
+------
+
+**Citation**
+
+Surveying the relative impact of mRNA features on local ribosome profiling read density in 28 datasets.
+Patrick O'Connor, Dmitry Andreev, Pavel Baranov
+bioRxiv doi: http://dx.doi.org/10.1101/018762
+
+   </help>
+ 
+</tool>
diff -r 000000000000 -r f40b0b26e766 synergy_31.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/synergy_31.xml	Tue Oct 20 13:05:05 2015 +0100
@@ -0,0 +1,33 @@
+<tool id="synergy_31" name="Synergism detection" version="1">
+     <description>(Step 2)</description>
+    <requirements>
+        <requirement type="package" version="0.1.0">RUST</requirement>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+    </requirements>
+    <command>python \${RUST_PATH}/synergy_31.py $observed_amino $observed_tripeptide $output1 </command>
+   <inputs>
+     <param format="csv" name="observed_amino" type="data" label="Amino acid metafootprint" help="RUST codon metafootprint analysis"/>
+     <param format="csv" name="observed_tripeptide" type="data" label="Tripeptide metafootprint" help="RUST tripeptide metafootprint analysis" />
+   </inputs>
+   <outputs>
+     <data format="csv" name="output1" />
+   </outputs>
+ 
+
+ 
+   <help>
+**What it does**
+
+Compares the observed RUST ratios for tripeptides to that expected based on that obtained with amino acids to detect cases of synergism in adjacent residues. Returns a csv file with the best candidates for synergism.
+
+------
+
+**Citation**
+
+Surveying the relative impact of mRNA features on local ribosome profiling read density in 28 datasets.
+Patrick O'Connor, Dmitry Andreev, Pavel Baranov
+bioRxiv doi: http://dx.doi.org/10.1101/018762
+
+   </help>
+ 
+</tool>
diff -r 000000000000 -r f40b0b26e766 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 20 13:05:05 2015 +0100
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="RUST" version="0.1.0">
+        <install version="1.0">
+            <actions>
+                <action type="setup_virtualenv">RUST==0.1.0</action>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="RUST_PATH">$INSTALL_DIR/venv/lib/python2.7/site-packages/RUST</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>          
+        </readme>
+    </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>
+</tool_dependency>