comparison cmbuild.xml @ 13:ffa96097e5b2 draft

Uploaded

12:c17ed5a530d2

    <description>from sequence alignments (cmbuild)</description>
    <parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" shared_inputs="" merge_outputs="cmfile_outfile"></parallelism>
    <requirements>
        <requirement type="package">infernal</requirement>
        <requirement type="package" version="1.1">infernal</requirement>
        <requirement type="package" version="8.21">gnu_coreutils</requirement>
    </requirements>
    <command>
        cmbuild 
            #if $is_summery_output:
                -o $summary_outfile
            #end if
            
            ## to many outputs, is that one really needed?
            ##-O $annotated_source_alignment_outfile

            $model_construction_opts.model_construction_opts_selector
            #if $model_construction_opts.model_construction_opts_selector == '--fast':

                $cyk
            #end if

            $cmfile_outfile
            $alignment_infile
            
    </command>
        <inputs>
            <!-- Stockholm or SELEX 
            SELEX is defined in EMBOSS datatypes
            -->
            <param name="alignment_infile" type="data" format="stockholm,selex" label="Sequence database"/>

            <conditional name="model_construction_opts">
                <param name="model_construction_opts_selector" type="select" label="These options control how consensus columns are defined in an alignment" help="">
                    <option value="--fast" selected="true">automatic (--fast)</option>
                    <option value="--hand">user defined (--hand)</option>
                </param>
                <when value="--fast">
                    <param name="symfrac" type="float" value="0.5" size="5" 
                        label="Define the residue fraction threshold necessary to define a consensus (--symfrac)" help=""/>
                </when>
                <when value="--hand"/>
            </conditional>

            <param name="noss" truevalue="--noss" falsevalue="" checked="False" type="boolean" 
                label="Ignore the secondary structure annotation, if any, in your multiple alignment file (--noss)" help=""/>

            <conditional name="relative_weights_opts">
                <param name="relative_weights_opts_selector" type="select" label="Options controlling relative weights" help="">
                    <option value="--wpb" selected="true">Henikoff (--wgb)</option>

                <when value="--wpb"/>
                <when value="--wgsc"/>
                <when value="--wnone"/>
                <when value="--wgiven"/>
                <when value="--wblosum">
                    <param name="wid" type="float" value="0.5" size="5" 
                        label="Percent identity for clustering the alignment (--wid)" help=""/>
                </when>
            </conditional>

                    <option value="--eent" selected="true">entropy weighting strategy (--eent)</option>
                    <option value="--enone">Turn off the entropy weighting strategy (--enone)</option>
                </param>
                <when value="--enone"/>
                <when value="--eent">
                    <param name="ere" type="float" value="0.59" size="5" 
                        label="Set the target mean match state relative entropy (--ere)" help=""/>

                    <param name="eminseq" type="integer" value="" size="5" 
                        label="Define the minimum allowed effective sequence number (--eminseq)" help=""/>

                    <param name="ehmmre" type="float" value="" size="5" 
                        label="Set the target HMM mean match state relative entropy (--ehmmre)" help=""/>

                    <param name="eset" type="integer" value="" size="5" 
                        label="Set the effective sequence number for entropy weighting (--eset)" help=""/>
                </when>
            </conditional>

                        <when value="--gibbs">
                            <param name="random_seed" type="integer" value="0" label="Randam Seed" help="" />
                        </when>
                    </conditional>

                    <param name="l" truevalue="-l" falsevalue="" checked="False" type="boolean" 
                        label="Turn on the local alignment algorithm" help="... which allows the alignment to span two or more subsequences if necessary"/>

                    <param name="notrunc" truevalue="--notrunc" falsevalue="" checked="False" type="boolean" 
                        label="Turn off the truncated alignment algorithm" help=""/>

                    <param name="cyk" type="select" label="Options for refining the input alignment" help="">
                        <option value="" selected="true">optimal accuracy algorithm</option>
                        <option value="--cyk">align with the CYK algorithm</option>
                    </param>

                    <param name="refine_output" truevalue="" falsevalue="" checked="False" type="boolean" 
                        label="Output the refined alignment file as it is used to build the covariance model" help=""/>

                </when>
            </conditional>


            <param name="is_summery_output" truevalue="" falsevalue="" checked="False" type="boolean" 
                label="Output a summery file?" help=""/>

        </inputs>
    <outputs>

            </filter>
        </data>

    </outputs>
    <help>


**What it does**

For each multiple sequence alignment build a covariance model.

How do I cite Infernal?
-----------------------

The Infernal 1.0 paper (Nawrocki et al., 2009) is the best paper to reference. 
If you’re writing for an enlightened (url-friendly) journal, you may want to cite the webpage
http://infernal.janelia.org/ because it is kept up-to-date. We hope to publish a paper related to
Infernal version 1.1 soon.

**Galaxy Wrapper Author**::

    *  Bjoern Gruening, University of Freiburg

    </help>
</tool>

13:ffa96097e5b2

    <description>from sequence alignments (cmbuild)</description>
    <parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" shared_inputs="" merge_outputs="cmfile_outfile"></parallelism>
    <requirements>
        <requirement type="package">infernal</requirement>
        <requirement type="package" version="1.1">infernal</requirement>
        <requirement type="package" version="8.22">gnu_coreutils</requirement>
    </requirements>
    <command>
<![CDATA[
        cmbuild
            #if $is_summery_output:
                -o $summary_outfile
            #end if

            ## to many outputs, is that one really needed?
            ##-O $annotated_source_alignment_outfile

            $model_construction_opts.model_construction_opts_selector
            #if $model_construction_opts.model_construction_opts_selector == '--fast':

                $cyk
            #end if

            $cmfile_outfile
            $alignment_infile

]]>
    </command>
        <inputs>
            <!-- Stockholm or SELEX
            SELEX is defined in EMBOSS datatypes
            -->
            <param name="alignment_infile" type="data" format="stockholm,selex" label="Sequence database"/>

            <conditional name="model_construction_opts">
                <param name="model_construction_opts_selector" type="select" label="These options control how consensus columns are defined in an alignment" help="">
                    <option value="--fast" selected="true">automatic (--fast)</option>
                    <option value="--hand">user defined (--hand)</option>
                </param>
                <when value="--fast">
                    <param name="symfrac" type="float" value="0.5" size="5"
                        label="Define the residue fraction threshold necessary to define a consensus (--symfrac)" help=""/>
                </when>
                <when value="--hand"/>
            </conditional>

            <param name="noss" truevalue="--noss" falsevalue="" checked="False" type="boolean"
                label="Ignore the secondary structure annotation, if any, in your multiple alignment file (--noss)" help=""/>

            <conditional name="relative_weights_opts">
                <param name="relative_weights_opts_selector" type="select" label="Options controlling relative weights" help="">
                    <option value="--wpb" selected="true">Henikoff (--wgb)</option>

                <when value="--wpb"/>
                <when value="--wgsc"/>
                <when value="--wnone"/>
                <when value="--wgiven"/>
                <when value="--wblosum">
                    <param name="wid" type="float" value="0.5" size="5"
                        label="Percent identity for clustering the alignment (--wid)" help=""/>
                </when>
            </conditional>

                    <option value="--eent" selected="true">entropy weighting strategy (--eent)</option>
                    <option value="--enone">Turn off the entropy weighting strategy (--enone)</option>
                </param>
                <when value="--enone"/>
                <when value="--eent">
                    <param name="ere" type="float" value="0.59" size="5"
                        label="Set the target mean match state relative entropy (--ere)" help=""/>

                    <param name="eminseq" type="integer" value="" size="5"
                        label="Define the minimum allowed effective sequence number (--eminseq)" help=""/>

                    <param name="ehmmre" type="float" value="" size="5"
                        label="Set the target HMM mean match state relative entropy (--ehmmre)" help=""/>

                    <param name="eset" type="integer" value="" size="5"
                        label="Set the effective sequence number for entropy weighting (--eset)" help=""/>
                </when>
            </conditional>

                        <when value="--gibbs">
                            <param name="random_seed" type="integer" value="0" label="Randam Seed" help="" />
                        </when>
                    </conditional>

                    <param name="l" truevalue="-l" falsevalue="" checked="False" type="boolean"
                        label="Turn on the local alignment algorithm" help="... which allows the alignment to span two or more subsequences if necessary"/>

                    <param name="notrunc" truevalue="--notrunc" falsevalue="" checked="False" type="boolean"
                        label="Turn off the truncated alignment algorithm" help=""/>

                    <param name="cyk" type="select" label="Options for refining the input alignment" help="">
                        <option value="" selected="true">optimal accuracy algorithm</option>
                        <option value="--cyk">align with the CYK algorithm</option>
                    </param>

                    <param name="refine_output" truevalue="" falsevalue="" checked="False" type="boolean"
                        label="Output the refined alignment file as it is used to build the covariance model" help=""/>

                </when>
            </conditional>


            <param name="is_summery_output" truevalue="" falsevalue="" checked="False" type="boolean"
                label="Output a summery file?" help=""/>

        </inputs>
    <outputs>

            </filter>
        </data>

    </outputs>
    <help>
<![CDATA[


**What it does**

For each multiple sequence alignment build a covariance model.

How do I cite Infernal?
-----------------------

The recommended citation for using Infernal 1.1 is E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches , Bioinformatics 29:2933-2935 (2013).

**Galaxy Wrapper Author**::

    *  Bjoern Gruening, University of Freiburg

]]>
    </help>
</tool>