diff hmmcv.xml @ 0:559e11a57c3e draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmcv.xml	Fri Oct 20 04:34:18 2017 -0400
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+<tool id="hmmcv" name="hmmcv" version="@VERSION@.1">
+    <description>
+        HMMCV is a tool for visualization of comparisons between hidden markov models (HMM)
+    </description>
+   <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version" />
+    <command detect_errors="aggressive"><![CDATA[
+    HMMCV
+        @COMMON_ARGS@
+        -m $model_filepath
+        -r $hmmcompare_file
+    ]]></command>
+
+    <inputs>
+        <param name="model_filepath" type="data" format="hmm" label="Input model"/>
+        <param name="hmmcompare_file" type="data" format="hmmcompare" label="Input comparison"/>
+        <section name="common" title="Common parameters">
+            <expand macro="common_parameters" />
+        </section>
+    </inputs>
+    <outputs>
+        <expand macro="vis_output"/>
+    </outputs>
+    <tests>
+      <test>
+        <param name="model_filepath" value="hammerheadClan.hmm" />
+        <param name="hmmcompare_file" value="input.hmmcompare" />
+        <param name="output_format" value="pdf" />
+        <param name="model_details" value="detailed" />
+        <param name="emission_layout" value="bar" />
+        <output_collection name="output_pdfs" type="list">
+          <element name="Hammerhead_1" file="Hammerhead_1.pdf" ftype="pdf" compare="sim_size" delta="50000"/>
+          <element name="Hammerhead_3" file="Hammerhead_3.pdf" ftype="pdf" compare="sim_size" delta="50000" />
+        </output_collection>
+      </test>
+    </tests>
+    <help><![CDATA[ **HMMCV -- Visualisation of Hidden Markov Models comparisons**
+    **Input.**
+    Hidden Markov Models in HMMER3 format, comparison file in hmmcompare format.
+    Optionally a stockholm alignment for each input model can be provided.
+
+    **Output.**
+    Depending on the detail level, only nodes with index (minimal), nodes with emission probabilities and indices (simple)
+    or nodes with states, emission and transition probabilities is visualised. Nodes linked by input comparison data
+    between different families are highlighted with color labels. 
+    File in pdf,svg,png,ps format.
+    
+    For more information, see     
+    .. __: https://github.com/eggzilla/cmv
+    ]]>
+    </help>
+    <expand macro="citations" />
+</tool>