Mercurial > repos > cpt > cpt_mist3_wrapper
comparison cpt_mist3/mist3.xml @ 0:1a9603d09814 draft default tip
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| author | cpt |
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| date | Fri, 17 Jun 2022 02:58:50 +0000 |
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| -1:000000000000 | 0:1a9603d09814 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="edu.tamu.cpt.mist3" name="MIST v3" version="19.1.0.0"> | |
| 3 <description>Multiple Interrelated Sequence doT plotter.</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 <import>cpt-macros.xml</import> | |
| 7 </macros> | |
| 8 <requirements> | |
| 9 <requirement type="package" version="2.7">python</requirement> | |
| 10 <requirement type="package" version="1.76">biopython</requirement> | |
| 11 <requirement type="package" version="8.0.192">openjdk</requirement> | |
| 12 <requirement type="package" version="7.0.8_68">imagemagick</requirement> | |
| 13 <requirement type="package" version="9.18">ghostscript</requirement> | |
| 14 </requirements> | |
| 15 <command detect_errors="aggressive"> | |
| 16 $__tool_directory__/mist3.py | |
| 17 #set repeat_var_1 = '" "'.join([ str($var) for $var in $fasta_files ]) | |
| 18 --window "${window}" | |
| 19 --zoom "${zoom}" | |
| 20 --matrix "${matrix}" | |
| 21 --files_path $output.files_path | |
| 22 --plot_type $plot_type | |
| 23 | |
| 24 "$repeat_var_1" | |
| 25 > $output | |
| 26 </command> | |
| 27 <inputs> | |
| 28 <param help="Sequences to plot" label="file" name="fasta_files" type="data" format="fasta" multiple="True"/> | |
| 29 | |
| 30 <param name="plot_type" label="Plot Type" type="select"> | |
| 31 <option value="complete">[complete] Complete NxN plot</option> | |
| 32 <option value="1vn">[1vN] 1 genome versus the rest</option> | |
| 33 <option value="2up">[2up] Compare two genomes (see help)</option> | |
| 34 </param> | |
| 35 | |
| 36 <param help="How zoomed in the image is" label="zoom" name="zoom" type="integer" value="50" min="5"/> | |
| 37 | |
| 38 <param help="Window Size" label="window" name="window" type="integer" value="10" min="5"/> | |
| 39 | |
| 40 <param label="Comparison Matrix" name="matrix" type="select"> | |
| 41 <option value="blosum62">Blosum62</option> | |
| 42 <option selected="True" value="edna">Extended DNA</option> | |
| 43 <option value="ednaorig">Extended DNA (Original)</option> | |
| 44 <option value="pam250">Pam 250</option> | |
| 45 <option value="protidentity">Protein Identity</option> | |
| 46 </param> | |
| 47 | |
| 48 </inputs> | |
| 49 <outputs> | |
| 50 <data format="html" name="output" /> | |
| 51 </outputs> | |
| 52 <tests> | |
| 53 <test> | |
| 54 <param name="fasta_files" value="mist3_in.fasta"/> | |
| 55 <param name="plot_type" value="complete"/> | |
| 56 <param name="zoom" value="100"/> | |
| 57 <param name="window" value="20"/> | |
| 58 <param name="matrix" value="edna"/> | |
| 59 <output name="output" ftype="html"> | |
| 60 <assert_contents> | |
| 61 <has_text text="Mist Results"/> | |
| 62 <has_text text="Each section of mist output is now clickable to view a higher resolution version of that subsection"/> | |
| 63 </assert_contents> | |
| 64 </output> | |
| 65 </test> | |
| 66 </tests> | |
| 67 <help> | |
| 68 Multiple Interrlated Sequence doTplotter | |
| 69 ======================================== | |
| 70 | |
| 71 Uses a stripped down vesion of Gepard (Dr. Jan Krumsiek/HelmholtzZentrum/IBIS) for dot plotting. | |
| 72 | |
| 73 Plot Types | |
| 74 ---------- | |
| 75 | |
| 76 There are three main plot types: | |
| 77 | |
| 78 - **complete** does an N x N plot of each genome versus every other genome | |
| 79 - **1vN** The first genome in the list is compared to each other genome | |
| 80 - **2up** two-genome comparison | |
| 81 | |
| 82 - If you provide TWO files and are using a protein comparison matrix, then the invidual | |
| 83 protein sequences of both files will be compared in a "complete" style plot. | |
| 84 - Otherwise, the first two genomes encountered will be compared. | |
| 85 | |
| 86 Options | |
| 87 ------- | |
| 88 | |
| 89 **Zoom** | |
| 90 | |
| 91 Be careful with this option. It represents the number of bases to plot in | |
| 92 a single pixel. For large genomes, this can mean very large images, and | |
| 93 should be lowered appropriately. For a value of 50, 50 bases would be | |
| 94 considered a single pixel in the output image. For a 1 Mbp genome comparison | |
| 95 (say 5 x 200-kb phages), this would result in a 20,000 pixel image. | |
| 96 | |
| 97 </help> | |
| 98 <citations> | |
| 99 <expand macro="citation/gepard" /> | |
| 100 <expand macro="citation/mijalisrasche" /> | |
| 101 <citation type="bibtex"> | |
| 102 @unpublished{galaxyTools, | |
| 103 author = {A. Criscione}, | |
| 104 title = {CPT Galaxy Tools}, | |
| 105 year = {2019-2021}, | |
| 106 note = {https://github.com/tamu-cpt/galaxy-tools/} | |
| 107 } | |
| 108 </citation> | |
| 109 </citations> | |
| 110 </tool> |