comparison cmbuild.xml @ 4:c47a7c52ac4f draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 236abfe2af8034017994daea08079887e64b68c8

3:2c2c5e5e495b

<tool id="infernal_cmbuild" name="Build covariance models" version="1.1.0.1">
    <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':
                --symfrac $model_construction_opts.symfrac
            #end if

                $notrunc
                $cyk
            #end if

            $cmfile_outfile
            $alignment_infile

]]>
    </command>
        <inputs>
            <!-- Stockholm or SELEX
            SELEX is defined in EMBOSS datatypes

                    <param name="wid" type="float" value="0.5"
                        label="Percent identity for clustering the alignment (--wid)" help=""/>
                </when>
            </conditional>


            <conditional name="effective_opts">
                <param name="effective_opts_selector" type="select" label="Options controlling effective sequence number" help="">
                    <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"
                        label="Set the target mean match state relative entropy (--ere)" help=""/>

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


            <conditional name="refining_opts">
                <param name="refining_opts_selector" type="select" label="Options for refining the input alignment" help="">
                    <option value="" selected="true">No refinement</option>
                    <option value="--refine">refine the input alignment</option>

                        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>

        <data format="text" name="summary_outfile" label="cmbuild summary on ${on_string}">
            <filter>is_summery_output is True</filter>
        </data>
        <!--<data format="stockholm" name="annotated_source_alignment_outfile" label="Annotated alignment from ${on_string}"/>-->
        <data format="cm" name="cmfile_outfile" label="Covariance models from ${on_string}"/>

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


**What it does**

cmbuild belongs to the INFERNAL software package that allows you to make consensus RNA secondary structure profiles, and use them to search nucleic acid sequence databases for homologous RNAs, or to create new structure-based multiple sequence alignments.

cm build builds a covariance model of an RNA multiple alignment. cmbuild uses the consensus structure to determine the architecture of the CM.


**Input**

Input file is a multiple sequence alignment file in Stockholm or SELEX format, and must contain consensus secondary structure annotation.
cmbuild uses the consensus structure to determine the architecture of the CM.

Example: simple example of a multiple RNA sequence alignment with secondary structure annotation

# STOCKHOLM 1.0
tRNA1             GCGGAUUUAGCUCAGUUGGG.AGAGCGCCAGACUGAAGAUCUGGAGGUCC
tRNA2             UCCGAUAUAGUGUAAC.GGCUAUCACAUCACGCUUUCACCGUGGAGA.CC
tRNA3             UCCGUGAUAGUUUAAU.GGUCAGAAUGGGCGCUUGUCGCGUGCCAGA.UC
tRNA4             GCUCGUAUGGCGCAGU.GGU.AGCGCAGCAGAUUGCAAAUCUGUUGGUCC
tRNA5             GGGCACAUGGCGCAGUUGGU.AGCGCGCUUCCCUUGCAAGGAAGAGGUCA
#=GC SS_cons      <<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.....<


**Output**

The output of cmbuild contains information about the size of your input alignment (in aligned columns
and # of sequences), and about the size of the resulting model.

In addition to writing CM(s) to the output file, cmbuild also outputs a single line for each model created to stdout. 
Each line has the following fields: 
- aln: the index of the alignment used to build the CM 
- idx: the index of the CM in the output file
- name: the name of the CM
- nseq: the number of sequences in the alignment used to build the CM
- eff nseq: the effective number of sequences used to build the model
- alen: the length of the alignment used to build the CM

- description: description of the model/alignment.


**Options controlling model construction**


These options control how consensus columns are defined in an alignment.

  - *--fast*: Define consensus columns automatically as those that have a fraction >= symfrac of residues as opposed to gaps. (See below for the --symfrac option.) This is the default.
  - *--hand*: Use reference coordinate annotation (#=GC RF line, in Stockholm) to determine which columns are consensus, and which are inserts. Any non-gap character indicates a consensus column. (For example, mark consensus columns with ”x”, and insert columns with ”.”.)
  - *--symfrac*: Define the residue fraction threshold necessary to define a consensus column when not using --hand. The default is 0.5. The symbol fraction in each column is calculated after taking relative sequence weighting into account. Setting this to 0.0 means that every alignment column will be assigned as consensus, which may be useful in some cases. Setting it to 1.0 means that only columns that include 0 gaps will be assigned as consensus.

  - *--ere*: Set the target mean match state relative entropy. By default the target relative entropy per match position is 0.59 bits for models with at least 1 basepair and 0.38 for models with zero basepairs.
  - *--eminseq*: Define the minimum allowed effective sequence number.
  - *--ehmmre*: Set the target HMM mean match state relative entropy. Entropy for basepairing match states is calculated using marginalized basepair emission probabilities.
  - *--eset*: Set the effective sequence number for entropy weighting.



**Options for refining the input alignment**

  - *--refine*: Attempt to refine the alignment before building the CM using expectation-maximization (EM). A CM is first built from the initial alignment as usual. Then, the sequences in the alignment are realigned optimally (with the HMM banded CYK algorithm, optimal means optimal given the bands) to the CM, and a new CM is built from the resulting alignment. The sequences are then realigned to the new CM, and a new CM is built from that alignment. This is continued until convergence, specifically when the alignments for two successive iterations are not significantly different (the summed bit scores of all the sequences in the alignment changes less than 1% between two successive iterations).
  - *Turn on the local alignment algorithm*: allows the alignment to span two or more subsequences if necessary (e.g. if the structures of the query model and target sequence are only partially shared), allowing certain large insertions and deletions in the structure to be penalized differently than normal indels. The default is to globally align the query model to the target sequences.
  - *--gibbs sampling*: Modifies the behavior of --refine so Gibbs sampling is used instead of EM. The difference is that during the alignment stage the alignment is not necessarily optimal, instead an alignment (parsetree) for each sequences is sampled from the posterior distribution of alignments as determined by the Inside algorithm. Due to this sampling step --gibbs is non- deterministic, so different runs with the same alignment may yield different results. This is not true when --refine is used without the --gibbs option, in which case the final alignment and CM will always be the same. When --gibbs is enabled, the --seed "number" option can be used to seed the random number generator predictably, making the results reproducible. The goal of the --gibbs option is to help expert RNA alignment curators refine structural alignments by allowing them to observe alternative high scoring alignments.
  - *--Random seed*: Seed the random number generator with an integer >= 0. This option can only be used in combination with --gibbs. If the given number is nonzero, stochastic sampling of alignments will be reproducible; the same command will give the same results. If the given number is 0, the random number generator is seeded arbitrarily, and stochastic samplings may vary from run to run of the same command. The default seed is 0.
   - *--Turn off the truncated alignment algorithm*: With --refine, turn off the truncated alignment algorithm. There is more information on this in the cmalign manual page.
  - *--cyk algorithm*: With --refine, align with the CYK algorithm. By default the optimal accuracy algorithm is used. There is more information on this in the cmalign manual page.
  
 

For further questions please refere to the Infernal Userguide_.

.. _Userguide: http://selab.janelia.org/software/infernal/Userguide.pdf


]]>
    </help>
    
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt509</citation>
        <citation type="bibtex">
            @ARTICLE{bgruening_galaxytools,
                Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},

                title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
                url = {https://github.com/bgruening/galaxytools}
            }
        </citation>
    </citations>
    
</tool>

4:c47a7c52ac4f

<tool id="infernal_cmbuild" name="Build covariance models" version="1.1.0.2">
    <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 -F
            #if $is_summery_output:
                -o '$summary_outfile'
            #end if

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

                $notrunc
                $cyk
            #end if

            '$cmfile_outfile'
            '$alignment_infile'
      &&
      cmcalibrate
        -L 0.01 --cpu \${GALAXY_SLOTS:-2}
        '$cmfile_outfile'
]]>
    </command>
        <inputs>
            <!-- Stockholm or SELEX
            SELEX is defined in EMBOSS datatypes

                    <param name="wid" type="float" value="0.5"
                        label="Percent identity for clustering the alignment (--wid)" help=""/>
                </when>
            </conditional>

            <conditional name="effective_opts">
                <param name="effective_opts_selector" type="select" label="Options controlling effective sequence number" help="">
                    <option value="--eent" >entropy weighting strategy (--eent)</option>
                    <option value="--enone" selected="true">Turn off the entropy weighting strategy (--enone)</option>
                </param>
                <when value="--enone"/>
                <when value="--eent">
                    <param name="ere" type="float" value="0.59"
                        label="Set the target mean match state relative entropy (--ere)" help=""/>

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

            <conditional name="refining_opts">
                <param name="refining_opts_selector" type="select" label="Options for refining the input alignment" help="">
                    <option value="" selected="true">No refinement</option>
                    <option value="--refine">refine the input alignment</option>

                        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>
        <data format="text" name="summary_outfile" label="cmbuild summary on ${on_string}">
            <filter>is_summery_output is True</filter>
        </data>
        <!--<data format="stockholm" name="annotated_source_alignment_outfile" label="Annotated alignment from ${on_string}"/>-->
        <data format="cm" name="cmfile_outfile" label="Covariance models from ${on_string}"/>

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

**What it does**

cmbuild belongs to the INFERNAL software package that allows you to make consensus RNA secondary structure profiles, and use them to search nucleic acid sequence databases for homologous RNAs, or to create new structure-based multiple sequence alignments.

cm build builds a covariance model of an RNA multiple alignment. cmbuild uses the consensus structure to determine the architecture of the CM.

**Input**

Input file is a multiple sequence alignment file in Stockholm or SELEX format, and must contain consensus secondary structure annotation.
cmbuild uses the consensus structure to determine the architecture of the CM.

Example: simple example of a multiple RNA sequence alignment with secondary structure annotation

# STOCKHOLM 1.0

tRNA1             GCGGAUUUAGCUCAGUUGGG.AGAGCGCCAGACUGAAGAUCUGGAGGUCC

tRNA2             UCCGAUAUAGUGUAAC.GGCUAUCACAUCACGCUUUCACCGUGGAGA.CC

tRNA3             UCCGUGAUAGUUUAAU.GGUCAGAAUGGGCGCUUGUCGCGUGCCAGA.UC

tRNA4             GCUCGUAUGGCGCAGU.GGU.AGCGCAGCAGAUUGCAAAUCUGUUGGUCC

tRNA5             GGGCACAUGGCGCAGUUGGU.AGCGCGCUUCCCUUGCAAGGAAGAGGUCA

#=GC SS_cons      <<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.....<


**Output**

The output of cmbuild contains information about the size of your input alignment (in aligned columns
and # of sequences), and about the size of the resulting model.

In addition to writing CM(s) to the output file, cmbuild also outputs a single line for each model created to stdout.
Each line has the following fields:
- aln: the index of the alignment used to build the CM
- idx: the index of the CM in the output file
- name: the name of the CM
- nseq: the number of sequences in the alignment used to build the CM
- eff nseq: the effective number of sequences used to build the model
- alen: the length of the alignment used to build the CM

- description: description of the model/alignment.


**Options controlling model construction**

These options control how consensus columns are defined in an alignment.

  - *--fast*: Define consensus columns automatically as those that have a fraction >= symfrac of residues as opposed to gaps. (See below for the --symfrac option.) This is the default.
  - *--hand*: Use reference coordinate annotation (#=GC RF line, in Stockholm) to determine which columns are consensus, and which are inserts. Any non-gap character indicates a consensus column. (For example, mark consensus columns with ”x”, and insert columns with ”.”.)
  - *--symfrac*: Define the residue fraction threshold necessary to define a consensus column when not using --hand. The default is 0.5. The symbol fraction in each column is calculated after taking relative sequence weighting into account. Setting this to 0.0 means that every alignment column will be assigned as consensus, which may be useful in some cases. Setting it to 1.0 means that only columns that include 0 gaps will be assigned as consensus.

  - *--ere*: Set the target mean match state relative entropy. By default the target relative entropy per match position is 0.59 bits for models with at least 1 basepair and 0.38 for models with zero basepairs.
  - *--eminseq*: Define the minimum allowed effective sequence number.
  - *--ehmmre*: Set the target HMM mean match state relative entropy. Entropy for basepairing match states is calculated using marginalized basepair emission probabilities.
  - *--eset*: Set the effective sequence number for entropy weighting.

**Options for refining the input alignment**

  - *--refine*: Attempt to refine the alignment before building the CM using expectation-maximization (EM). A CM is first built from the initial alignment as usual. Then, the sequences in the alignment are realigned optimally (with the HMM banded CYK algorithm, optimal means optimal given the bands) to the CM, and a new CM is built from the resulting alignment. The sequences are then realigned to the new CM, and a new CM is built from that alignment. This is continued until convergence, specifically when the alignments for two successive iterations are not significantly different (the summed bit scores of all the sequences in the alignment changes less than 1% between two successive iterations).
  - *Turn on the local alignment algorithm*: allows the alignment to span two or more subsequences if necessary (e.g. if the structures of the query model and target sequence are only partially shared), allowing certain large insertions and deletions in the structure to be penalized differently than normal indels. The default is to globally align the query model to the target sequences.
  - *--gibbs sampling*: Modifies the behavior of --refine so Gibbs sampling is used instead of EM. The difference is that during the alignment stage the alignment is not necessarily optimal, instead an alignment (parsetree) for each sequences is sampled from the posterior distribution of alignments as determined by the Inside algorithm. Due to this sampling step --gibbs is non- deterministic, so different runs with the same alignment may yield different results. This is not true when --refine is used without the --gibbs option, in which case the final alignment and CM will always be the same. When --gibbs is enabled, the --seed "number" option can be used to seed the random number generator predictably, making the results reproducible. The goal of the --gibbs option is to help expert RNA alignment curators refine structural alignments by allowing them to observe alternative high scoring alignments.
  - *--Random seed*: Seed the random number generator with an integer >= 0. This option can only be used in combination with --gibbs. If the given number is nonzero, stochastic sampling of alignments will be reproducible; the same command will give the same results. If the given number is 0, the random number generator is seeded arbitrarily, and stochastic samplings may vary from run to run of the same command. The default seed is 0.
   - *--Turn off the truncated alignment algorithm*: With --refine, turn off the truncated alignment algorithm. There is more information on this in the cmalign manual page.
  - *--cyk algorithm*: With --refine, align with the CYK algorithm. By default the optimal accuracy algorithm is used. There is more information on this in the cmalign manual page.

For further questions please refere to the Infernal Userguide_.

.. _Userguide: http://selab.janelia.org/software/infernal/Userguide.pdf

]]>
    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt509</citation>
        <citation type="bibtex">
            @ARTICLE{bgruening_galaxytools,
                Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},

                title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
                url = {https://github.com/bgruening/galaxytools}
            }
        </citation>
    </citations>
</tool>