comparison cmstat.xml @ 5:6e18e0b098cd draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86

4:c47a7c52ac4f

<tool id="infernal_cmstat" name="Summary statistics" version="1.1.0.1">
    <description>for covariance model (cmstat)</description>
    <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[
        ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
        ## it will be converted to a tab delimited file and piped to Galaxy
        temp_tabular_output=\$(mktemp);

        cmstat

            #if str($cm_opts.cm_opts_selector) == "db":
                $cm_opts.database.fields.path
            #else:
                $cm_opts.cmfile
            #end if

            > \$temp_tabular_output
            ;

            ## 1. replace all lines starting # (comment lines)
            ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
            sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile

]]>
    </command>
        <inputs>
            <conditional name="cm_opts">

            </conditional>
        </inputs>
    <outputs>
        <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
    </outputs>
    <help>
<![CDATA[


**What it does**

     target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”.
(12) Mean relative entropy per match state, in bits, if the CM were transformed into an HMM (information from structure is ignored). The larger the difference between the CM and HMM
     relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.


For further questions please refere to the Infernal `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},
                keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
                title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
                url = {https://github.com/bgruening/galaxytools}
            }
        </citation>
    </citations>
  
    
</tool>

5:6e18e0b098cd

<tool id="infernal_cmstat" name="cmstat" version="@VERSION@.0">
    <description>Summary statistics for covariance model </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio" />
    <command>
<![CDATA[
        ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
        ## it will be converted to a tab delimited file and piped to Galaxy
        ##temp_tabular_output=\$(mktemp);

        cmstat
            #if str($cm_opts.cm_opts_selector) == "db":
                $cm_opts.database.fields.path
            #else:
                $cm_opts.cmfile
            #end if

            > $outfile


]]>
    </command>
        <inputs>
            <conditional name="cm_opts">

            </conditional>
        </inputs>
    <outputs>
        <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <conditional name="cm_opts">
                <param name="cm_opts_selector" value="histdb"/>
                <param name="cmfile" value="cmstat_input.cm"/>
            </conditional>
            <output name="outfile" >
                <assert_contents>
                    <has_text text="idx"/>
                    <has_text text="accession"/>
                    <has_text text="nseq"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[


**What it does**

     target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”.
(12) Mean relative entropy per match state, in bits, if the CM were transformed into an HMM (information from structure is ignored). The larger the difference between the CM and HMM
     relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.


For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_.

]]>
    </help>
    <expand macro="citations" />

</tool>