comparison inforna.xml @ 0:1c441b2843c8 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty

0:1c441b2843c8

<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>
    </requirements>
    <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>
    <command>
<![CDATA[
    InfoRNA
        $rna_sec_structure
        -c $seq_constraints
        -F $obj_function
        -p $prob_bad_mutation
        -n $max_violations
]]>
    </command>
    <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="Constraint Overview" help="" />
        <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="m" selected="true">mfe (default)</option>
                <option value="mp">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="" />
        <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>
<![CDATA[
**What it does**

INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. 

http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp

**Input**

Constraints: RNA Secondary Structure, Sequence Constraints and Allowed Violations

]]>

    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btl194</citation>
    </citations>
</tool>