Mercurial > repos > scottx611x > clodius
comparison clodius.xml @ 0:8a435cbdfe3f draft
planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
author | scottx611x |
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date | Tue, 03 Oct 2017 13:44:15 -0400 |
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1 <?xml version='1.0' encoding='utf-8'?> | |
2 | |
3 <tool id="clodius" name="clodius" version="0.0.1"> | |
4 <description>Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.</description> | |
5 <requirements> | |
6 <requirement type="package" version="0.3.2">pybigwig</requirement> | |
7 <requirement type="package" version="0.2.19">negspy</requirement> | |
8 <requirement type="package" version="1.0.7">slugid</requirement> | |
9 <requirement type="package" version="0.6.5">clodius</requirement> | |
10 </requirements> | |
11 <command> | |
12 <![CDATA[ | |
13 clodius aggregate $file_type $input_file --assembly $genome_assembly | |
14 | |
15 #if $output_filename: | |
16 --output-file $output_filename | |
17 #end if | |
18 | |
19 #if $file_type == "bedpe": | |
20 --chr1-col $chromosome_one_column | |
21 --from1-col $from_one_column | |
22 --to1-col $to_one_column | |
23 --chr2-col $chromosome_two_column | |
24 --from2-col $from_two_column | |
25 --to2-col $to_two_column | |
26 #end if | |
27 | |
28 #if $file_type == "bedfile": | |
29 --max-per-tile $max_per_tile | |
30 --importance-column $importance_column | |
31 #if $delimiter == "tab": | |
32 --delimiter '\t' | |
33 #end if | |
34 #end if | |
35 | |
36 #if $file_type == "bedgraph": | |
37 #if $chromosome_column: | |
38 --chromosome-col $chromosome_column | |
39 #end if | |
40 | |
41 #if $from_position_column: | |
42 --from-pos-col $from_position_column | |
43 #end if | |
44 | |
45 #if $to_position_column: | |
46 --to-pos-col $to_position_column | |
47 #end if | |
48 | |
49 #if $value_column: | |
50 --value-col $value_column | |
51 #end if | |
52 | |
53 #if $has_header: | |
54 --has-header | |
55 #end if | |
56 | |
57 #if $nan_value: | |
58 --nan-value $nan_value | |
59 #end if | |
60 #end if | |
61 ]]> | |
62 </command> | |
63 <inputs> | |
64 <param | |
65 name="chromosome_column" | |
66 type="integer" | |
67 label="The column number (1-based) which contains the chromosome name." | |
68 optional="true"/> | |
69 <param | |
70 name="chromosome_one_column" | |
71 type="integer" | |
72 label="The column containing the first chromosome." | |
73 optional="true"/> | |
74 <param | |
75 name="chromosome_two_column" | |
76 type="integer" | |
77 label="The column containing the second chromosome." | |
78 optional="true"/> | |
79 <param | |
80 name="delimiter" | |
81 type="text" | |
82 optional="true"/> | |
83 <param | |
84 name="file_type" | |
85 type="text" | |
86 label="Filetype to be aggregated"> | |
87 <option value="bedpe">Bedpe-like file</option> | |
88 <option value="bedfile">Gene Annotation File</option> | |
89 <option value="bedgraph">BedGraph file</option> | |
90 <option value="bigwig">BigWig File</option> | |
91 </param> | |
92 <param | |
93 name="from_one_column" | |
94 type="integer" | |
95 label="The column containing the first start position." | |
96 optional="true"/> | |
97 <param | |
98 name="from_two_column" | |
99 type="integer" | |
100 label="The column containing the second start position." | |
101 optional="true"/> | |
102 <param | |
103 name="from_position_column" | |
104 type="integer" | |
105 label="The column number (1-based) which contains the starting position." | |
106 value="2"/> | |
107 <param | |
108 name="genome_assembly" | |
109 type="text" | |
110 label="Genome Assembly" | |
111 value="hg19"/> | |
112 <param | |
113 name="has_header" | |
114 type="boolean" | |
115 label="Does this file have a header that we should ignore?" | |
116 optional="true"/> | |
117 <param | |
118 name="input_file" | |
119 type="data" | |
120 label="File to be aggregated"/> | |
121 <param | |
122 name="importance_column" | |
123 type="integer" | |
124 label="The column (1-based) containing information about how important that row is. | |
125 If it's absent, then use the length of the region. | |
126 If the value is equal to `random`, then a random value will be used for the importance (effectively leading to random sampling)" | |
127 optional="true"/> | |
128 <param | |
129 name="max_per_tile" | |
130 type="integer" | |
131 label="Max per tile." | |
132 value="100"/> | |
133 <param | |
134 name="nan_value" | |
135 type="text" | |
136 label="The string to use as a NaN value." | |
137 optional="true"/> | |
138 <param | |
139 name="output_filename" | |
140 type="text" | |
141 label="The default output file name to use. If this isn't specified, clodius will replace the current extension with something resonable." | |
142 optional="true"/> | |
143 <param | |
144 name="to_one_column" | |
145 type="integer" | |
146 label="The column containing the first end position." | |
147 optional="true"/> | |
148 <param | |
149 name="to_two_column" | |
150 type="integer" | |
151 label="The column containing the second end position." | |
152 optional="true"/> | |
153 <param | |
154 name="to_position_column" | |
155 type="integer" | |
156 label="The column number (1-based) which contains the ending position." | |
157 value="3"/> | |
158 <param | |
159 name="value_column" | |
160 type="integer" | |
161 label="The column number (1-based) which contains the actual value position." | |
162 value="4"/> | |
163 </inputs> | |
164 <outputs> | |
165 <data name="output_file" /> | |
166 </outputs> | |
167 <tests> | |
168 <test expect_num_outputs="1" expect_exit_code="0"> | |
169 <param name="input_file" value="Rao_RepA_GM12878_Arrowhead.txt"/> | |
170 <param name="file_type" value="bedpe" /> | |
171 <param name="chromosome_one_column" value="1" /> | |
172 <param name="chromosome_two_column" value="1" /> | |
173 <param name="from_one_column" value="2" /> | |
174 <param name="from_two_column" value="2" /> | |
175 <param name="to_one_column" value="3" /> | |
176 <param name="to_two_column" value="3" /> | |
177 <param name="output_filename" value="bedpe_test.out" /> | |
178 <output name="output_file" file="Rao_RepA_GM12878_Arrowhead.txt.multires" /> | |
179 </test> | |
180 <test expect_num_outputs="1" expect_exit_code="0"> | |
181 <param name="input_file" value="geneAnnotationsExonsUnions.short.bed" /> | |
182 <param name="file_type" value="bedfile" /> | |
183 <param name="importance_column" value="5" /> | |
184 <param name="max_per_tile" value="20" /> | |
185 <param name="output_filename" value="bedfile_test.out" /> | |
186 </test> | |
187 <test expect_num_outputs="1" expect_exit_code="0"> | |
188 <param name="input_file" value="cnvs_hw.tsv" /> | |
189 <param name="file_type" value="bedgraph" /> | |
190 <param name="genome_assembly" value="grch37" /> | |
191 <param name="chromosome_column" value="2" /> | |
192 <param name="from_position_column" value="3" /> | |
193 <param name="to_position_column" value="4" /> | |
194 <param name="value_column" value="5" /> | |
195 <param name="has_header" value="true" /> | |
196 <param name="nan_value" value="NA" /> | |
197 <param name="output_filename" value="bedgraph_test.out" /> | |
198 </test> | |
199 <test expect_num_outputs="1" expect_exit_code="0"> | |
200 <param name="input_file" value="test.bw" /> | |
201 <param name="file_type" value="bigwig" /> | |
202 <param name="output_filename" value="bigwig_test.out" /> | |
203 <output name="output_file" file="test.multires.bw" lines_diff="9"/> | |
204 </test> | |
205 </tests> | |
206 <help> | |
207 <![CDATA[ | |
208 **What it does** | |
209 Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer. | |
210 ]]> | |
211 </help> | |
212 </tool> |