changeset 6:9ac5311c2e49 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/inforna.xml	Fri May 16 06:29:21 2014 -0400
@@ -0,0 +1,41 @@
+<tool id="inforna" name="InfoRNA" version="0.1.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="1.0">inforna</requirement>
+        <requirement type="package" version="2.1.5">vienna_rna</requirement>
+        <requirement type="set_environment">INFORNA_SCRIPT_PATH</requirement>
+    </requirements>
+    <command>
+InfoRNA
+    </command>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+    </stdio>
+    <inputs>
+        <param format="txt" name="rna_sec_structure" type="text" label="RNA Secondary Structure" help="folding temperature is fixed at 37°C" />
+        <param format="txt" name="seq_constraints" type="text" area="true" size="10x40" label="Sequence Constraints and Allowed Violations: (IUPAC symbols)" help="(e.g.: '4 W +' constrains the sequence to have a 'A' or a 'U' at position 4, but due to the '+', this constraint is allowed to be violated) " />
+        <param format="txt" name="constr_overview" type="text" area="true" size="10x40" label="Sequence Constraints and Allowed Violations: (IUPAC symbols)" help="(e.g.: '4 W +' constrains the sequence to have a 'A' or a 'U' at position 4, but due to the '+', this constraint is allowed to be violated) " />
+        <param name="max_violations" label="Maximal number of violations" type="integer" value="1" help="(in the designed sequence)" />
+    
+         
+        <param name="obj_function" type="select" multiple="False" label="Objective function" help="-t">
+                        <option value="mfe" selected="true">mfe (default)</option>
+                        <option value="mfe->prob">mfe-&gt;prob ... only for (structures &lt;= 200)</option>
+        </param>
+        <param name="prob_bad_mutation" label="Probability for accepting bad mutations" type="float" value="0.1" help="" />
+        <param name="presort" type="boolean" checked="true" truevalue="--noLP" falsevalue="" label="Pre-sort candidates for mutation" help="--noLP" />
+        <param name="num_design_seq" label="Number of Designed Sequences" type="integer" value="1" help="(Sequences might be very similar, which is due to the rather fixed initializing sequence.)" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="ps" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>**What it does**
+    http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp
+    
+INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. Here, you can get an example of the settings and the results.
+
+    </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri May 16 06:29:21 2014 -0400
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="INFORNA_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+    <package name="vienna_rna" version="2.1.5">
+        <repository changeset_revision="9d5a8bae2e8a" name="package_vienna_rna_2_1" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="inforna" version="1.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://www.bioinf.uni-freiburg.de/Software/INFO-RNA/versions/INFO-RNA-2.1.2.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="9d5a8bae2e8a" name="package_vienna_rna_2_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="vienna_rna" version="2.1.5" />
+                    </repository>
+                </action>
+                <action type="shell_command">make VIENNA=\$ROOT_VIENNA_RNA_DIR LDFLAGS="-L\$ROOT_VIENNA_RNA_DIR/lib -lRNA -fopenmp" </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+                
+            </actions>
+        </install>
+        <readme>Compiling InfoRNA requires a C compiler (typically gcc)</readme>
+    </package>
+</tool_dependency>