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comparison crispr_studio.xml @ 0:ad4ae405cdc1 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ commit d746438ee434696f2867394eca7a93d6ec704320"
author iuc
date Wed, 14 Aug 2019 11:37:32 -0400
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1 <?xml version="1.0"?>
2 <tool id="crispr_studio" name="CRISPR Studio" version="1+galaxy0">
3 <description>
4 facilitate and accelerate CRISPR array visualization from a GFF3 file generated with CRISPRDetect
5 </description>
6 <requirements>
7 <requirement type="package" version="1">crispr_studio</requirement>
8 </requirements>
9 <command detect_errors="exit_code">
10 <![CDATA[
11 ln -s '${input_data}' ./infile &&
12
13 #if $rerun.r == '-r':
14 ln -s '${rerun.prev_final}' infile.fasta_fasta36.spacermatch.mcl.final &&
15 ln -s '${rerun.prev_svg}' infile.fasta_fasta36.spacermatch.mcl.svg &&
16 #end if
17
18 CRISPR_Studio
19
20 #if $order.s_order == 'File':
21 -l '${order.isolate_list}'
22 #else:
23 -s '${order.s_order}'
24 #end if
25
26 $f
27 $n
28 $gU
29 $gS
30 $rerun.r
31
32 #if $cut_off:
33 -c '${cut_off}'
34 #end if
35
36 -i ./infile
37 ]]></command>
38 <inputs>
39 <param name="input_data" type="data" format="gff" label="Input sequences" help="gff (GFF3) files are valid"/>
40 <conditional name="order">
41 <param name='s_order' type="select" label="Order of Isolates" help="Determine order of isolates in figure (-s)">
42 <option value="DistMatrix" selected="True">DistMatrix (Order extracted from a distance matrix based on the similarity of the arrays in the isolates.)</option>
43 <option value="CRISPRDetect">CRISPRDetect (Order in GFF File)</option>
44 <option value="File">By File</option>
45 </param>
46 <when value="DistMatrix">
47 </when>
48 <when value="CRISPRDetect">
49 </when>
50 <when value="File">
51 <param name="isolate_list" type="data" format="txt" optional="true" label="List of Isolates to show" help="Generate the figure with the subset of isolates listed in the file"/>
52 </when>
53 </conditional>
54 <param name="n" argument="-n" truevalue="-n" falsevalue="" type="boolean" label="Show the size of the spacers over the boxed diamonds?" help="We recommend to use this option only for experimental analysis of the data"/>
55 <param argument="-f" truevalue="-f" falsevalue="" type="boolean" label="Skip the verification of the fasta file generated from the GFF file?" help="The verification is mainly based on the length of the spacer sequences. If a spacer is 1.5 time shorter or longer than the average spacer size of the dataset, a warning is raised and the script stops (Verification is ran by default)."/>
56 <param name="cut_off" type="integer" optional="true" label="Score cutoff for pairing of the spacers"/>
57 <param argument="-gU" truevalue="-gU" falsevalue="" type="boolean" label="Gray out unique?" help="The unique spacers will be grayed"/>
58 <param argument="-gS" truevalue="-gS" falsevalue="" type="boolean" label="Gray out similar?" help="The conserved spacers will be grayed"/>
59 <conditional name="rerun">
60 <param argument="-r" type="select" label="Change spacer colour?" help="Use this option to keep the same color attributed to the spacer during a previous analysis">
61 <option value="">No</option>
62 <option value="-r">Yes</option>
63 </param>
64 <when value="-r">
65 <param name="prev_final" format="tabular" label="Previous spacer.mcl.final" type="data" help="Input a previous .final file you want to retain the colour from"/>
66 <param name="prev_svg" format="svg" label="Previous SVG" type="data" help="Input a previous .svg file you want to retain the colour from"/>
67 </when>
68 <when value="">
69 </when>
70 </conditional>
71 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs">
72 <option value="out_fasta36">Fasta36</option>
73 <option value="out_spacermatch">Spacermatch</option>
74 <option value="out_spacermatch_mcl">Spacermatch MCL</option>
75 <option value="out_spacermatch_mcl_col">Spacermatch MCL Col</option>
76 </param>
77
78 </inputs>
79 <outputs>
80 <data name="output_fasta" format="tabular" label="${tool.name} on ${on_string}: fasta output" from_work_dir="infile.fasta"/>
81 <data name="output_fasta36" format="tabular" label="${tool.name} on ${on_string}: fasta_fast36 output" from_work_dir="infile.fasta_fasta36">
82 <filter>outputs and 'out_fasta36' in outputs</filter>
83 </data>
84 <data name="output_spacermatch" format="tabular" label="${tool.name} on ${on_string}: spacermatch output" from_work_dir="infile.fasta_fasta36.spacermatch">
85 <filter>outputs and 'out_spacermatch' in outputs</filter>
86 </data>
87 <data name="output_spacermatch_mcl" format="tabular" label="${tool.name} on ${on_string}: spacermatch.mcl output" from_work_dir="infile.fasta_fasta36.spacermatch.mcl">
88 <filter>outputs and 'out_spacermatch_mcl' in outputs</filter>
89 </data>
90 <data name="output_spacermatch_mcl_col" format="tabular" label="${tool.name} on ${on_string}: spacermatch.mcl.col output" from_work_dir="infile.fasta_fasta36.spacermatch.mcl.col">
91 <filter>outputs and 'out_spacermatch_mcl_col' in outputs</filter>
92 </data>
93 <data name="output_spacermatch_mcl_final" format="tabular" label="${tool.name} on ${on_string}: spacematch.mcl.final output" from_work_dir="infile.fasta_fasta36.spacermatch.mcl.final"/>
94 <data name="output_svg" format="svg" label="${tool.name} on ${on_string}: SVG output" from_work_dir="infile.fasta_fasta36.spacermatch.mcl.svg"/>
95 </outputs>
96 <tests>
97 <test expect_num_outputs="7">
98 <param name="input_data" value="crispr_test.gff" ftype="gff"/>
99 <param name="outputs" value="out_fasta36,out_spacermatch,out_spacermatch_mcl_col,out_spacermatch_mcl"/>
100 <output name="output_fasta" file="crispr_test.gff.fasta"/>
101 <output name="output_fasta36">
102 <assert_contents>
103 <has_text text="NC_010473"/>
104 </assert_contents>
105 </output>
106 <output name="output_spacermatch" file="crispr_test.gff.fasta_fasta36.spacermatch"/>
107 <output name="output_spacermatch_mcl" file="crispr_test.gff.fasta_fasta36.spacermatch.mcl"/>
108 <output name="output_spacermatch_mcl_col">
109 <assert_contents>
110 <has_text text="NC_010473"/>
111 </assert_contents>
112 </output>
113 <output name="output_spacermatch_mcl_final">
114 <assert_contents>
115 <has_text text="NC_010473"/>
116 </assert_contents>
117 </output>
118 <output name="output_svg">
119 <assert_contents>
120 <has_text text="svg"/>
121 </assert_contents>
122 </output>
123 </test>
124 <test expect_num_outputs="3">
125 <param name="input_data" value="crispr_test_adv.gff" ftype="gff"/>
126 <param name="isolate_list" value="test_isolates.txt" ftype="txt"/>
127 <param name="n" value="true"/>
128 <output name="output_fasta" file="crispr_test_adv.gff.fasta"/>
129 <output name="output_spacermatch_mcl_final">
130 <assert_contents>
131 <has_text text="NC_010473"/>
132 </assert_contents>
133 </output>
134 <output name="output_svg">
135 <assert_contents>
136 <has_text text="svg"/>
137 </assert_contents>
138 </output>
139 </test>
140 </tests>
141 <help><![CDATA[
142
143 **What it does**
144
145 CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization.
146 It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code
147 to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.
148
149 ]]>
150 </help>
151 <citations>
152 <citation type="bibtex">
153 @UNPUBLISHED{moineaulab2018,
154 author = {moineaulab},
155 title = {CRISPRStudio: Program developed to facilitate and accelerate CRISPR array visualization},
156 year = {2018},
157 url = {https://github.com/moineaulab/CRISPRStudio},
158 }
159 </citation>
160 </citations>
161 </tool>