diff cmv.xml @ 0:6baa763b77ba 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/cmv.xml	Fri Oct 20 04:26:28 2017 -0400
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+<tool id="cmv" name="cmv" version="@VERSION@.1">
+  <description>
+    CMV is a tool for visualization of RNA family models, also known as covariance models (CM)
+  </description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  
+  <expand macro="requirements" />
+
+  <expand macro="stdio" />
+  
+  <expand macro="version" />
+  <command><![CDATA[
+  CMV
+        @COMMON_ARGS@
+        -m $model_filepath 
+  ]]></command>
+  
+  <inputs>
+    <param name="model_filepath" type="data" format="cm" label="Input model"/>
+    <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="Hammerhead_HH9.cm" />
+      <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_HH9" file="Hammerhead_HH9.pdf" ftype="pdf" compare="sim_size" />
+      </output_collection>
+    </test>
+  </tests>
+  <help><![CDATA[
+  **CMV -- Visualisation of RNA family models**
+
+  **Input.**
+  Covariance Models in INFERNAL 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 node type and indices (simple)
+  or nodes with states, emission and transition probabilities are 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>