comparison cmstat.xml @ 13:ffa96097e5b2 draft

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12:c17ed5a530d2

<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="8.21">gnu_coreutils</requirement>
    </requirements>
    <command>
        ## 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

            ## 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">
                <param name="cm_opts_selector" type="select" label="Subject covariance models">
                  <option value="db" selected="True">Locally installed covariance models</option>

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


**What it does**

The cmstat utility prints out a tabular file of summary statistics for each given covariance model.

Output format
-------------

By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a
tabular format. 

The columns are:

(1) The index of this profile, numbering each on in the file starting from 1.
(2) The name of the profile.

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

<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

            ## 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">
                <param name="cm_opts_selector" type="select" label="Subject covariance models">
                  <option value="db" selected="True">Locally installed covariance models</option>

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


**What it does**

The cmstat utility prints out a tabular file of summary statistics for each given covariance model.

Output format
-------------

By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a
tabular format.

The columns are:

(1) The index of this profile, numbering each on in the file starting from 1.
(2) The name of the profile.

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>