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annotate cmpress.xml @ 5:6e18e0b098cd draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author bgruening
date Sat, 21 Jan 2017 17:36:57 -0500
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children c9e29ac5d099
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1 <tool id="infernal_cmpress" name="cmpress" version="@VERSION@.0">
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2 <description> Prepare a covariance model database for cmscan</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 ## CM file from the history or stored as database on disc
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11 #if str($cm_opts.cm_opts_selector) == "db":
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12 cmfile_path='$cm_opts.database.fields.path'
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13 #else:
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14 ##'$cm_opts.cmfile'
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15 cmfile_path='$cmfile'
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16 #end if
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17 &&
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18 cmpress -F "\$cmfile_path" &&
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19 ##cmpress creates four files in the same directory of the cm file
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20 cd `dirname "\$cmfile_path"` &&
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21 tar -cvf '$outfile' `basename "\$cmfile_path"`.i1*
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22 ]]>
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23 </command>
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24 <inputs>
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25 <conditional name="cm_opts">
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26 <param name="cm_opts_selector" type="select" label="Subject covariance models &lt;cmdb&gt; ">
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27 <option value="db" >Locally installed covariance models</option>
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28 <option value="histdb" selected="True">Covariance model from your history</option>
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29 </param>
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30 <when value="db">
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31 <param name="database" type="select" label="Covariance models">
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32 <options from_file="infernal.loc">
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33 <column name="value" index="0"/>
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34 <column name="name" index="1"/>
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35 <column name="path" index="2"/>
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36 </options>
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37 </param>
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38 </when>
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39 <when value="histdb">
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40 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
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41 </when>
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42 </conditional>
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43
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44 </inputs>
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45 <outputs>
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46 <data format="tar" name="outfile" label="cmpress on ${on_string}"/>
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47 </outputs>
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48
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49 <tests>
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50 <test>
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51 <conditional name="cm_opts">
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52 <param name="cm_opts_selector" value="histdb"/>
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53 <param name="cmfile" value="cmpress_input_minifam.cm"/>
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54 </conditional>
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55 <assert_stdout>
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56 <has_text text="Working... done."/>
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57 </assert_stdout>
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58
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59 </test>
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61 </tests>
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62 <help>
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63 <![CDATA[
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66 **What it does**
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68 Starting from a CM database <cmfile> in standard Infernal-1.1 format, construct binary compressed datafiles for cm-
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69 scan. The cmpress step is required for cmscan to work.
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71 **Input format**
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73 The <cmfile> must be have already been calibrated with cmcalibrate for cmpress to work.
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75 **Output format**
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79 For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_.
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82 ]]>
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83 </help>
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85 <expand macro="citations" />
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88 </tool>