diff cpt_mist3/mist3.xml @ 0:1a9603d09814 draft default tip

Uploaded

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+++ b/cpt_mist3/mist3.xml	Fri Jun 17 02:58:50 2022 +0000
@@ -0,0 +1,110 @@
+<?xml version="1.0"?>
+<tool id="edu.tamu.cpt.mist3" name="MIST v3" version="19.1.0.0">
+	<description>Multiple Interrelated Sequence doT plotter.</description>
+	<macros>
+		<import>macros.xml</import>
+		<import>cpt-macros.xml</import>
+	</macros>
+	<requirements>
+		<requirement type="package" version="2.7">python</requirement>
+                <requirement type="package" version="1.76">biopython</requirement>
+		<requirement type="package" version="8.0.192">openjdk</requirement>
+		<requirement type="package" version="7.0.8_68">imagemagick</requirement>
+		<requirement type="package" version="9.18">ghostscript</requirement>
+	</requirements>
+	<command detect_errors="aggressive">
+$__tool_directory__/mist3.py
+#set repeat_var_1 = '" "'.join([ str($var) for $var in $fasta_files ])
+--window "${window}"
+--zoom "${zoom}"
+--matrix "${matrix}"
+--files_path $output.files_path
+--plot_type $plot_type
+
+"$repeat_var_1"
+> $output
+</command>
+	<inputs>
+		<param help="Sequences to plot" label="file" name="fasta_files" type="data" format="fasta" multiple="True"/>
+
+		<param name="plot_type" label="Plot Type" type="select">
+			<option value="complete">[complete] Complete NxN plot</option>
+			<option value="1vn">[1vN] 1 genome versus the rest</option>
+			<option value="2up">[2up] Compare two genomes (see help)</option>
+		</param>
+
+		<param help="How zoomed in the image is" label="zoom" name="zoom" type="integer" value="50" min="5"/>
+
+		<param help="Window Size" label="window" name="window" type="integer" value="10" min="5"/>
+
+		<param label="Comparison Matrix" name="matrix" type="select">
+			<option value="blosum62">Blosum62</option>
+			<option selected="True" value="edna">Extended DNA</option>
+			<option value="ednaorig">Extended DNA (Original)</option>
+			<option value="pam250">Pam 250</option>
+			<option value="protidentity">Protein Identity</option>
+		</param>
+
+	</inputs>
+	<outputs>
+		<data format="html" name="output" />
+	</outputs>
+	<tests>
+		<test>
+			<param name="fasta_files" value="mist3_in.fasta"/>
+			<param name="plot_type" value="complete"/>
+			<param name="zoom" value="100"/>
+			<param name="window" value="20"/>
+			<param name="matrix" value="edna"/>
+			<output name="output" ftype="html">
+				<assert_contents>
+					<has_text text="Mist Results"/>
+					<has_text text="Each section of mist output is now clickable to view a higher resolution version of that subsection"/>
+				</assert_contents>
+			</output>
+		</test>
+	</tests>
+	<help>
+Multiple Interrlated Sequence doTplotter
+========================================
+
+Uses a stripped down vesion of Gepard (Dr. Jan Krumsiek/HelmholtzZentrum/IBIS) for dot plotting.
+
+Plot Types
+----------
+
+There are three main plot types:
+
+- **complete** does an N x N plot of each genome versus every other genome
+- **1vN** The first genome in the list is compared to each other genome
+- **2up** two-genome comparison
+
+	- If you provide TWO files and are using a protein comparison matrix, then the invidual 
+		protein sequences of both files will be compared in a "complete" style plot.
+	- Otherwise, the first two genomes encountered will be compared.
+
+Options
+-------
+
+**Zoom**
+
+Be careful with this option. It represents the number of bases to plot in
+a single pixel. For large genomes, this can mean very large images, and
+should be lowered appropriately. For a value of 50, 50 bases would be
+considered a single pixel in the output image. For a 1 Mbp genome comparison
+(say 5 x 200-kb phages), this would result in a 20,000 pixel image.
+
+</help>
+	<citations>
+		<expand macro="citation/gepard" />
+		<expand macro="citation/mijalisrasche" />
+                <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {A. Criscione},
+				title = {CPT Galaxy Tools},
+				year = {2019-2021},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+                        </citation>
+	</citations>
+</tool>