annotate hmmcv.xml @ 1:ef8be69b8e9e draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 108e83ea251bee3b952cb49ef758e69294608c1d
author rnateam
date Wed, 02 Jan 2019 10:17:46 -0500
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1 <tool id="hmmcv" name="hmmcv" version="@VERSION@">
0
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2 <description>
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3 HMMCV is a tool for visualization of comparisons between hidden markov models (HMM)
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version" />
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11 <command detect_errors="aggressive"><![CDATA[
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12 HMMCV
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13 @COMMON_ARGS@
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14 -m $model_filepath
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15 -r $hmmcompare_file
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16 ]]></command>
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17
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18 <inputs>
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19 <param name="model_filepath" type="data" format="hmm" label="Input model"/>
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20 <param name="hmmcompare_file" type="data" format="hmmcompare" label="Input comparison"/>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
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21 <section name="common" title="Common parameters">
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22 <expand macro="common_parameters" />
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23 </section>
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24 </inputs>
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25 <outputs>
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26 <expand macro="vis_output"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="model_filepath" value="hammerheadClan.hmm" />
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31 <param name="hmmcompare_file" value="input.hmmcompare" />
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32 <param name="output_format" value="pdf" />
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33 <param name="model_details" value="detailed" />
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34 <param name="emission_layout" value="bar" />
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35 <output_collection name="output_pdfs" type="list">
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36 <element name="Hammerhead_1" file="Hammerhead_1.pdf" ftype="pdf" compare="sim_size" delta="50000"/>
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37 <element name="Hammerhead_3" file="Hammerhead_3.pdf" ftype="pdf" compare="sim_size" delta="50000" />
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38 </output_collection>
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39 </test>
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40 </tests>
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41 <help><![CDATA[ **HMMCV -- Visualisation of Hidden Markov Models comparisons**
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42 **Input.**
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43 Hidden Markov Models in HMMER3 format, comparison file in hmmcompare format.
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44 Optionally a stockholm alignment for each input model can be provided.
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45
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46 **Output.**
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47 Depending on the detail level, only nodes with index (minimal), nodes with emission probabilities and indices (simple)
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48 or nodes with states, emission and transition probabilities is visualised. Nodes linked by input comparison data
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49 between different families are highlighted with color labels.
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50 File in pdf,svg,png,ps format.
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51
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52 For more information, see
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53 .. __: https://github.com/eggzilla/cmv
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54 ]]>
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55 </help>
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56 <expand macro="citations" />
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57 </tool>