diff cofold.xml @ 0:65fff071414e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cofold.xml	Wed Jan 14 08:56:58 2015 -0500
@@ -0,0 +1,136 @@
+<tool id="cofold" name="Cofold" version="0.0.1">
+    <description>An RNA secondary structure prediction method that takes co-transcriptional folding into account</description>
+    <requirements>
+        <requirement type="package" version="0.0.1"></requirement>
+    </requirements>
+    <version_command>CoFold --version</version_command>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+    <command interpreter="python">
+<![CDATA[
+        cofold.py
+            -i $infile
+            -o1 $tabularFile
+            --parameters " -T$temperature -d$dangling
+                -P $energy_parameter
+                --distAlpha $distAlpha
+                --distTau $distTau
+                #if $advancedOptions.advancedSelector == 'yes':
+                    $advancedOptions.constraint
+                    $advancedOptions.noconversion
+                    $advancedOptions.nolp
+                    $advancedOptions.nogu
+                    $advancedOptions.noclosinggu
+                    $advancedOptions.notetra
+                    $advancedOptions.circular
+                #end if
+            ";
+        count=`ls -l *.ps | wc -l`;
+        echo '#RNA structures: '\$count > $report;
+]]>
+    </command>
+    <inputs>
+        <param format="fasta" name="infile" type="data" label="FASTA file"/>
+        <param name="distAlpha" type="float" value="0.5" label="temperature [°C]" help="(--distAlpha)"/>
+        <param name="distTau" type="float" value="640.0" label="temperature [°C]" help="(--distTau)"/>
+        <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="(-T)"/>
+        <param name="energy_parameter" type="select" label="Thermodynamic energy parameters" help="(-P)">
+            <option value="rna_turner1999.par" selected="True">Turner 1999</option>
+            <option value="rna_turner2004.par">Turner 2004</option>
+            <option value="rna_andronescu2007.par">Andronescu 2007</option>
+        </param>
+        <param name="dangling" type="select" label="how to treat dangling end energies" help="(-d)">
+            <option value="0">0: ignore dangling ends</option>
+            <option value="1">1: unpaired bases participate in one dangling end only</option>
+            <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
+            <option value="3">3: allow coaxial stacking</option>
+        </param>
+        <conditional name="advancedOptions">
+            <param name="advancedSelector" type="select" label="Advanced Options">
+                <option value="no">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="yes">
+                <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false"
+                    label="Calculate structures subject to constraints" help="(--constraint)"/>
+                <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false"
+                    label="No conversion" help="Do not convert thymine to uracile (T -> U). (--noconv)"/>
+                <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false"
+                    label="No lonely pairs" help="--noLP  don't allow lonely pairs. (--noLP)"/>
+                <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false"
+                    label="No GU pairing" help="Don't allow pairing of G and U. (--noGU)"/>
+                <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false"
+                    label="No GU pairing at the ends" help="Don't allow pairing of G and U at the ends of helices. (--noClosingGU)"/>
+                <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false"
+                    label="No stabilization for loops, hairpins etc." help="(--noTetra)"/>
+                <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false"
+                    label="Assume circular RNA structure" help="(--circ)"/>
+                <param name="noPS" type="boolean" truevalue="--noPS" falsevalue="" checked="false"
+                    label="Don't generate PS files" help="(--noPS)"/>
+            </when>
+            <when value="no" />
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="tabularFile" format="tabular" label="Tabular File"/>
+        <data name="report" format="txt" label="RNA PS File" hidden="true">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.ps" ext="rna_eps" visible="true"/>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="cofold1.fasta" ftype="fasta"/>
+            <param name="noPS" value="--noPS"/>
+            <output name="tabularFile" file="colfold_results1.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="infile" value="cofold1.fasta" ftype="fasta"/>
+            <param name="noPS" value="--noPS"/>
+            <param name="energy_parameter" value="rna_andronescu2007.par"/>
+            <param name="dangling" value="1"/>
+            <param name="advancedSelector" value="yes"/>
+            <output name="tabularFile" file="colfold_results2.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="infile" value="cofold1.fasta" ftype="fasta"/>
+            <param name="noPS" value=""/>
+            <output name="tabularFile" file="colfold_results3.tabular" ftype="tabular" />
+            <output name="report">
+                <assert_contents>
+                    <has_line_matching expression="#RNA structures.*" />
+                </assert_contents>
+                <discovered_dataset designation="example1_ss" file="example1_ss.ps" compare="sim_size" delta="100" ftype="rna_eps"/>
+            </output>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**CoFold**
+
+A tool for prediction of RNA secondary structure that takes co-transcriptional folding into account 
+
+**Input format**
+
+CoFold requires one input file in FASTA format.
+
+------
+
+**Outputs**
+
+- Tab-seperated file
+    - 1st column: header line of FASTA input
+    - 2nd column: sequence
+    - 3rd column: dot-bracket notation
+    - 4th column: free energy
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">doi:10.1093/nar/gkt174</citation>
+        <citation type="doi">doi:10.1093/nar/gks241</citation>
+    </citations>
+</tool>