diff observed_expected.xml @ 0:f40b0b26e766 default tip

First commit

--- /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>