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date Mon, 05 Jun 2023 02:41:13 +0000
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1 <tool id="edu.tamu.cpt2.gbk_viz.easyfig" name="Easyfig:" version="2.2.3">
2 <description> Galaxy wrapper for genbank visualization</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>cpt-macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="aggressive"><![CDATA[
9 IFS=',' read -r -a genList <<< "$gbkIn";
10 IFS=' ' read -r -a revList <<< "$revString";
11 lenGBK=\${#genList[@]};
12 lenREV=\${#revList[@]};
13 for (( i=0; i<\$lenGBK; i++ )); do
14 for (( j=0; j<\$lenREV; j++ )); do
15 if [[ \$((i+1)) -eq revList[\$j] ]]; then
16 genList[\$i]="\${genList[\$i]} R";
17 fi
18 done;
19 done;
20
21 python '$__tool_directory__/Easyfig.py'
22 -e '$eVal'
23 #if $blast.input_type == "files":
24 -blast_files
25 #for $file in $blast.blastIn:
26 '$file'
27 #end for
28 #else if $blast.input_type == "blastN":
29 -blastn
30 $blast.keepBlast
31 #else if $blast.input_type == "blastX":
32 -tblastx
33 '$blast.keepBlast'
34 #end if
35 -aln '$align'
36 -i '$identity'
37 -min_length '$blastLen'
38 -legend '$leg'
39 -leg_name '$nameLoc'
40 -f1 '$tfF'
41 -f2 '$intF'
42 -blast_col '$color'
43 #if $gc != "":
44 -G '$gc'
45 #end if
46
47 -o '$SVG_Out'
48 -svg
49 -filter
50 \${genList[@]}
51 #if $blast.input_type != "files"
52 #if $blast.keepBlast
53 &&
54 tar -cvf tempTar temp_easyfig
55 &&
56 mv tempTar '$blastDir'
57 #end if
58 #end if
59 ]]></command>
60 <inputs>
61 <param label="Genbanks" name="gbkIn" type="data" multiple="true" format="genbank"/>
62 <param label="Reverse Items (See 'Reverse Option' in help text)" name="revString" type="text" value=""/>
63 <conditional name="blast">
64 <param name="input_type" type="select" label="Choose BLAST file source/generation: ">
65 <option value="files" selected="true">Use existing BLAST result</option>
66 <option value="blastN">Auto-run blastN</option>
67 <option value="blastX">Auto-run tblastX</option>
68 </param>
69 <when value="files">
70 <param label="Blast Results (12-Column .tsv)" name="blastIn" type="data" format="tabular" multiple="True"/>
71 </when>
72 <when value="blastN">
73 <param name="keepBlast" type="boolean" checked="false" label="Keep generated blast results" truevalue="-keep" falsevalue=""/>
74 </when>
75 <when value="blastX">
76 <param name="keepBlast" type="boolean" checked="false" label="Keep generated blast results" truevalue="-keep" falsevalue=""/>
77 </when>
78 </conditional>
79 <param label="Minimum E Value" name="eVal" type="float" value="0.001"/>
80 <param label="Minimum Percent Identity Value" name="identity" type="float" value="0.00"/>
81 <param label="Minimum Length for Blast Hit to be drawn" name="blastLen" type="integer" value="0"/>
82 <param label="Draw colour gradient figure for blast hits." name="tfF" type="boolean" checked="false" truevalue="T" falsevalue="F"/>
83 <param label="How many base pairs long to draw the scale legend item (0 to not draw it)" name="intF" type="integer" value="0"/>
84 <param label="Customize location of gene name" name="leg" type="select">
85 <option value="single">Single</option>
86 <option value="double">Double</option>
87 <option value="top">Top</option>
88 <option value="bottom">Bottom</option>
89 <option value="both">Both</option>
90 <option value="None">None</option>
91 </param>
92 <param label="What property to get feature name from" name="nameLoc" type="text" value="gene"/>
93 <param label="Customize alignment for Blast hits" name="align" type="select">
94 <option value="best">Best</option>
95 <option value="left">Left</option>
96 <option value="right">Right</option>
97 <option value="centre">Center</option>
98 </param>
99 <param label="Customize color for Blast hits" name="color" type="select">
100 <option value="gray">Gray</option>
101 <option value="red">Red</option>
102 <option value="blue">Blue</option>
103 </param>
104 <param label="Select GC Content plot" name="gc" type="select">
105 <option value="">No GC</option>
106 <option value="GCContent">GC Content</option>
107 <option value="GCSkew">GC Skew</option>
108 </param>
109 <param name="out_format" type="select" label="Output data type">
110 <option value="svg">SVG</option>
111 <option value="html">HTML</option>
112 </param>
113 </inputs>
114 <outputs>
115 <data format="svg" name="SVG_Out" label="Easyfig Output">
116 <change_format>
117 <when input="out_format" value="html" format="html"/>
118 </change_format>
119 </data>
120 <data format="tar.gz" name="blastDir" label="Easyfig-generated Blast data">
121 <filter>blast['input_type'] != 'files'</filter>
122 <filter>blast['keepBlast']</filter>
123 </data>
124 </outputs>
125 <help><![CDATA[
126 **What it does**
127
128 EasyFig Version 2.2.3 generates a linear genomic comparison of 1 to an infinite number of GenBank/EMBL files as a customizable graphic output.
129
130 **Input**
131 An input GenBank or EMBL file must have source line, or Sequence.
132 ' source 1..<sequence length>' or 'FT source 1..<sequence length>'
133 Only 'CDS' features will be recorded.
134
135
136 **Reverse Option**
137 Easyfig can plot a genbank file in reverse, effectively inverting the sequence and its annotations. Specify which genbanks to reverse
138 by providing their list index position in the Reverse Items field. The list is in order from the bottom-up, so if three genbanks are selected,
139 the bottom-most one is 1, the middle is 2, and the top-most 3.
140 The numbers must be separated by a space. Entering "2 3" will reverse the middle and top items, and the bottom "1" will be read in the forward orientation.
141
142
143 **Nucleotide BLAST**
144 - run BLASTn, run tBLASTx, or provide 12-column BLAST results for each input.
145
146
147 **General options**
148 - E-value: Select the minimum e-value of blast hits to be drawn. Default is 0.001
149
150 - Percent identity: Enter the minimum hit percent identity to be drawn. Default is 0.
151
152 - Hit length: Enter the minimum length of similarity (in nucleotides) for the output to be included on the drawing.
153
154 - BLAST scale: Toggle the BLAST similarity scale key for display.
155
156 - Genome scale bar: Enter a value in base pairs for the length of scale bar. Default is zero, which does not draw a scale bar.
157
158 - Position for feature labels : single (single column), double (two columns), top (feature labels of top genome drawn above figure), bottom (feature labels from bottom genome drawn below figure), both (top and bottom genome features drawn above and below figure), none (no legend or gene labelling, default)
159
160 - Source of feature label: default is gene. Other options include the product tag.
161
162 - Alignment: align the graphic according to best/left/right/center. Alignment of genomes best aligns feature file perpendicular to best blast hit. Default is center.
163
164 - BLAST similarity gradient color: options are gray, red, and blue.
165
166 - GCContent plot: select to display GC content or GCSkew graphs with the output.
167
168
169 **Output**
170 A Scalable Vector Graphics (svg) file or static html display are returned.
171
172
173 Blast Wrapper written by Criscione, Anthony, Center for Phage Technology, Texas A&M University, 2020
174 ]]></help>
175 <expand macro="citations">
176 <citation type="doi">10.1093/bioinformatics/btr039</citation>
177 </expand>
178 </tool>