Mercurial > repos > rnateam > hmmcv
diff hmmcv.xml @ 0:559e11a57c3e draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
author | rnateam |
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date | Fri, 20 Oct 2017 04:34:18 -0400 |
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children | ef8be69b8e9e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hmmcv.xml Fri Oct 20 04:34:18 2017 -0400 @@ -0,0 +1,57 @@ +<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>