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annotate cmpress.xml @ 9:1d74ed49cf41 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
author bgruening
date Mon, 11 Nov 2024 10:27:19 +0000
parents c9e29ac5d099
children
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1 <tool id="infernal_cmpress" name="cmpress" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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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="xrefs"/>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <command detect_errors="aggressive">
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10 <![CDATA[
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11 mkdir -p ./cm_model &&
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12 #if str($cm_opts.cm_opts_selector) == "db":
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13 ln -s '$cm_opts.database.fields.path' ./cm_model/
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14 #else:
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15 ln -s '$cmfile' ./cm_model/
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16 #end if
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17 &&
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18 cmpress -F ./cm_model/* &&
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19 cd ./cm_model/ &&
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20 tar -cvf '$outfile' *.i1f *.i1i *.i1m *.i1p
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21 ]]>
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22 </command>
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23 <inputs>
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24 <expand macro="DB" />
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25 </inputs>
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26 <outputs>
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27 <data format="tar" name="outfile" label="cmpress on ${on_string}"/>
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28 </outputs>
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30 <tests>
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31 <test>
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32 <conditional name="cm_opts">
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33 <param name="cm_opts_selector" value="histdb"/>
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34 <param name="cmfile" value="cmpress_input_minifam.cm"/>
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35 </conditional>
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36 <assert_stdout>
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37 <has_text text="Working... done."/>
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38 </assert_stdout>
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40 </test>
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41 <test>
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42 <conditional name="cm_opts">
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43 <param name="cm_opts_selector" value="db"/>
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44 <param name="database" value="cmpress_input_minifam.cm"/>
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45 </conditional>
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46 <assert_stdout>
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47 <has_text text="Working... done."/>
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48 </assert_stdout>
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49
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50 </test>
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51 </tests>
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52 <help>
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53 <![CDATA[
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56 **What it does**
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58 Starting from a CM database <cmfile> in standard Infernal-1.1 format, construct binary compressed datafiles for cm-
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59 scan. The cmpress step is required for cmscan to work.
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61 **Input format**
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63 The <cmfile> must be have already been calibrated with cmcalibrate for cmpress to work.
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65 **Output format**
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69 For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_.
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72 ]]>
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73 </help>
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75 <expand macro="citations" />
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78 </tool>