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comparison cummerbund_to_tabular.xml @ 0:648c27c78eed draft

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Initial commit with version 1.0.0 of the tool.
author devteam
date Tue, 23 Dec 2014 16:01:24 -0500
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children 36f917aa4b60
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1 <?xml version="1.0"?>
2 <tool id="cummerbund_to_cuffdiff" name="Extract CuffDiff" version="1.0.0">
3 <description>tabular files from a cummeRbund database</description>
4 <command interpreter="python"><![CDATA[
5 cummerbund_to_tabular.py --file ${input_database}
6 ${cds_count} ${cds_diff} ${cds_exp_diff} ${cds_fpkm} ${cds_rg}
7 ${gene_exp_diff} ${genes_count} ${genes_fpkm} ${gene_rg} ${isoform_exp_diff}
8 ${isoform_count} ${isoform_fpkm} ${isoform_rg} ${promoters_diff} ${read_groups}
9 ${run_info} ${splicing_diff} ${tss_group_exp} ${tss_count_tracking} ${tss_fpkm}
10 ${tss_rg} ${var_model}
11 ]]></command>
12 <inputs>
13 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
14 <param type="boolean" name="cds_count" truevalue="--tables cds_count" falsevalue="" label="CDS count tracking" />
15 <param type="boolean" name="cds_diff" truevalue="--tables cds_diff" falsevalue="" label="CDS overloading diffential expression testing" />
16 <param type="boolean" name="cds_exp_diff" truevalue="--tables cds_exp_diff" falsevalue="" label="CDS FPKM differential expression testing" />
17 <param type="boolean" name="cds_fpkm" truevalue="--tables cds_fpkm" falsevalue="" label="CDS FPKM tracking" />
18 <param type="boolean" name="cds_rg" truevalue="--tables cds_rg" falsevalue="" label="CDS read groups" />
19 <param type="boolean" name="gene_exp_diff" truevalue="--tables gene_exp_diff" falsevalue="" label="gene differential expression testing" />
20 <param type="boolean" name="genes_count" truevalue="--tables genes_count" falsevalue="" label="gene count tracking" />
21 <param type="boolean" name="genes_fpkm" truevalue="--tables genes_fpkm" falsevalue="" label="gene FPKM tracking" />
22 <param type="boolean" name="gene_rg" truevalue="--tables gene_rg" falsevalue="" label="gene read groups" />
23 <param type="boolean" name="isoform_exp_diff" truevalue="--tables isoform_exp_diff" falsevalue="" label="transcript differential expression testing" />
24 <param type="boolean" name="isoform_count" truevalue="--tables isoform_count" falsevalue="" label="transcript count tracking" />
25 <param type="boolean" name="isoform_fpkm" truevalue="--tables isoform_fpkm" falsevalue="" label="transcript FPKM tracking" />
26 <param type="boolean" name="isoform_rg" truevalue="--tables isoform_rg" falsevalue="" label="transcript read groups" />
27 <param type="boolean" name="promoters_diff" truevalue="--tables promoters_diff" falsevalue="" label="promoter differential testing" />
28 <param type="boolean" name="read_groups" truevalue="--tables read_groups" falsevalue="" label="Read Groups" />
29 <param type="boolean" name="run_info" truevalue="--tables run_info" falsevalue="" label="Run details" />
30 <param type="boolean" name="splicing_diff" truevalue="--tables splicing_diff" falsevalue="" label="splicing differential expression testing" />
31 <param type="boolean" name="tss_group_exp" truevalue="--tables tss_group_exp" falsevalue="" label="TSS groups differential expression testing" />
32 <param type="boolean" name="tss_count_tracking" truevalue="--tables tss_count_tracking" falsevalue="" label="TSS count FPKM tracking" />
33 <param type="boolean" name="tss_fpkm" truevalue="--tables tss_fpkm" falsevalue="" label="TSS groups FPKM tracking" />
34 <param type="boolean" name="tss_rg" truevalue="--tables tss_rg" falsevalue="" label="TSS read groups" />
35 <param type="boolean" name="var_model" truevalue="--tables var_model" falsevalue="" label="var_model.info" />
36 </inputs>
37 <outputs>
38 <data format="tabular" name="cds_count_output" from_work_dir="cds_count.tabular" label="${tool.name} on ${on_string}: CDS count tracking">
39 <filter>(cds_count is True)</filter>
40 </data>
41 <data format="tabular" name="cds_diff_output" from_work_dir="cds_diff.tabular" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
42 <filter>(cds_diff is True)</filter>
43 </data>
44 <data format="tabular" name="cds_exp_diff_output" from_work_dir="cds_exp_diff.tabular" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing">
45 <filter>(cds_exp_diff is True)</filter>
46 </data>
47 <data format="tabular" name="cds_fpkm_output" from_work_dir="cds_fpkm.tabular" label="${tool.name} on ${on_string}: CDS FPKM tracking">
48 <filter>(cds_fpkm is True)</filter>
49 </data>
50 <data format="tabular" name="cds_rg_output" from_work_dir="cds_rg.tabular" label="${tool.name} on ${on_string}: CDS read groups">
51 <filter>(cds_rg is True)</filter>
52 </data>
53 <data format="tabular" name="gene_exp_diff_output" from_work_dir="gene_exp_diff.tabular" label="${tool.name} on ${on_string}: gene differential expression testing">
54 <filter>(gene_exp_diff is True)</filter>
55 </data>
56 <data format="tabular" name="genes_count_output" from_work_dir="genes_count.tabular" label="${tool.name} on ${on_string}: gene count tracking">
57 <filter>(genes_count is True)</filter>
58 </data>
59 <data format="tabular" name="genes_fpkm_output" from_work_dir="genes_fpkm.tabular" label="${tool.name} on ${on_string}: gene FPKM tracking">
60 <filter>(genes_fpkm is True)</filter>
61 </data>
62 <data format="tabular" name="gene_rg_output" from_work_dir="gene_rg.tabular" label="${tool.name} on ${on_string}: gene read groups">
63 <filter>(gene_rg is True)</filter>
64 </data>
65 <data format="tabular" name="isoform_exp_diff_output" from_work_dir="isoform_exp_diff.tabular" label="${tool.name} on ${on_string}: transcript differential expression testing">
66 <filter>(isoform_exp_diff is True)</filter>
67 </data>
68 <data format="tabular" name="isoform_count_output" from_work_dir="isoform_count.tabular" label="${tool.name} on ${on_string}: transcript count tracking">
69 <filter>(isoform_count is True)</filter>
70 </data>
71 <data format="tabular" name="isoform_fpkm_output" from_work_dir="isoform_fpkm.tabular" label="${tool.name} on ${on_string}: transcript FPKM tracking">
72 <filter>(isoform_fpkm is True)</filter>
73 </data>
74 <data format="tabular" name="isoform_rg_output" from_work_dir="isoform_rg.tabular" label="${tool.name} on ${on_string}: transcript read groups">
75 <filter>(isoform_rg is True)</filter>
76 </data>
77 <data format="tabular" name="promoters_diff_output" from_work_dir="promoters_diff.tabular" label="${tool.name} on ${on_string}: promoter differential testing">
78 <filter>(promoters_diff is True)</filter>
79 </data>
80 <data format="tabular" name="read_groups_output" from_work_dir="read_groups.tabular" label="${tool.name} on ${on_string}: Read Groups">
81 <filter>(read_groups is True)</filter>
82 </data>
83 <data format="tabular" name="run_info_output" from_work_dir="run_info.tabular" label="${tool.name} on ${on_string}: Run details">
84 <filter>(run_info is True)</filter>
85 </data>
86 <data format="tabular" name="splicing_diff_output" from_work_dir="splicing_diff.tabular" label="${tool.name} on ${on_string}: splicing differential expression testing">
87 <filter>(splicing_diff is True)</filter>
88 </data>
89 <data format="tabular" name="tss_group_exp_output" from_work_dir="tss_group_exp.tabular" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
90 <filter>(tss_group_exp is True)</filter>
91 </data>
92 <data format="tabular" name="tss_count_tracking_output" from_work_dir="tss_count_tracking.tabular" label="${tool.name} on ${on_string}: TSS count FPKM tracking">
93 <filter>(tss_count_tracking is True)</filter>
94 </data>
95 <data format="tabular" name="tss_fpkm_output" from_work_dir="tss_fpkm.tabular" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
96 <filter>(tss_fpkm is True)</filter>
97 </data>
98 <data format="tabular" name="tss_rg_output" from_work_dir="tss_rg.tabular" label="${tool.name} on ${on_string}: TSS read groups">
99 <filter>(tss_rg is True)</filter>
100 </data>
101 <data format="tabular" name="var_model_output" from_work_dir="var_model.tabular" label="${tool.name} on ${on_string}: var_model.info">
102 <filter>(var_model is True)</filter>
103 </data>
104 </outputs>
105 <citations>
106 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
107 </citations>
108 <help>This tool extracts cuffdiff tabular files from a cummeRbund SQLite database.</help>
109 <tests>
110 <test>
111 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
112 <param name="cds_count" value="True" />
113 <param name="cds_diff" value="True" />
114 <param name="cds_exp_diff" value="True" />
115 <param name="cds_fpkm" value="True" />
116 <param name="cds_rg" value="True" />
117 <param name="gene_exp_diff" value="True" />
118 <param name="genes_count" value="True" />
119 <param name="genes_fpkm" value="True" />
120 <param name="gene_rg" value="True" />
121 <param name="isoform_exp_diff" value="True" />
122 <param name="isoform_count" value="True" />
123 <param name="isoform_fpkm" value="True" />
124 <param name="isoform_rg" value="True" />
125 <param name="promoters_diff" value="True" />
126 <param name="read_groups" value="True" />
127 <param name="run_info" value="True" />
128 <param name="splicing_diff" value="True" />
129 <param name="tss_group_exp" value="True" />
130 <param name="tss_count_tracking" value="True" />
131 <param name="tss_fpkm" value="True" />
132 <param name="tss_rg" value="True" />
133 <param name="var_model" value="True" />
134 <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" />
135 <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" />
136 <output name="cds_exp_diff_output" ftype="tabular" file="cds_exp_diff.tabular" />
137 <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" />
138 <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" />
139 <output name="gene_exp_diff_output" ftype="tabular" file="gene_exp_diff.tabular" />
140 <output name="genes_count_output" ftype="tabular" file="genes_count.tabular" />
141 <output name="genes_fpkm_output" ftype="tabular" file="genes_fpkm.tabular" />
142 <output name="gene_rg_output" ftype="tabular" file="gene_rg.tabular" />
143 <output name="isoform_exp_diff_output" ftype="tabular" file="isoform_exp_diff.tabular" />
144 <output name="isoform_count_output" ftype="tabular" file="isoform_count.tabular" />
145 <output name="isoform_fpkm_output" ftype="tabular" file="isoform_fpkm.tabular" />
146 <output name="isoform_rg_output" ftype="tabular" file="isoform_rg.tabular" />
147 <output name="promoters_diff_output" ftype="tabular" file="promoters_diff.tabular" />
148 <output name="read_groups_output" ftype="tabular" file="read_groups.tabular" />
149 <output name="run_info_output" ftype="tabular" file="run_info.tabular" />
150 <output name="splicing_diff_output" ftype="tabular" file="splicing_diff.tabular" />
151 <output name="tss_group_exp_output" ftype="tabular" file="tss_group_exp.tabular" />
152 <output name="tss_count_tracking_output" ftype="tabular" file="tss_count_tracking.tabular" />
153 <output name="tss_fpkm_output" ftype="tabular" file="tss_fpkm.tabular" />
154 <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" />
155 <output name="var_model_output" ftype="tabular" file="var_model.tabular" />
156 </test>
157 <test>
158 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
159 <param name="cds_count" value="True" />
160 <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" />
161 </test>
162 <test>
163 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
164 <param name="cds_diff" value="True" />
165 <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" />
166 </test>
167 <test>
168 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
169 <param name="cds_exp_diff" value="True" />
170 <output name="cds_exp_diff_output" ftype="tabular" file="cds_exp_diff.tabular" />
171 </test>
172 <test>
173 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
174 <param name="cds_fpkm" value="True" />
175 <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" />
176 </test>
177 <test>
178 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
179 <param name="cds_rg" value="True" />
180 <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" />
181 </test>
182 <test>
183 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
184 <param name="gene_exp_diff" value="True" />
185 <output name="gene_exp_diff_output" ftype="tabular" file="gene_exp_diff.tabular" />
186 </test>
187 <test>
188 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
189 <param name="genes_count" value="True" />
190 <output name="genes_count_output" ftype="tabular" file="genes_count.tabular" />
191 </test>
192 <test>
193 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
194 <param name="genes_fpkm" value="True" />
195 <output name="genes_fpkm_output" ftype="tabular" file="genes_fpkm.tabular" />
196 </test>
197 <test>
198 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
199 <param name="gene_rg" value="True" />
200 <output name="gene_rg_output" ftype="tabular" file="gene_rg.tabular" />
201 </test>
202 <test>
203 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
204 <param name="isoform_exp_diff" value="True" />
205 <output name="isoform_exp_diff_output" ftype="tabular" file="isoform_exp_diff.tabular" />
206 </test>
207 <test>
208 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
209 <param name="isoform_count" value="True" />
210 <output name="isoform_count_output" ftype="tabular" file="isoform_count.tabular" />
211 </test>
212 <test>
213 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
214 <param name="isoform_fpkm" value="True" />
215 <output name="isoform_fpkm_output" ftype="tabular" file="isoform_fpkm.tabular" />
216 </test>
217 <test>
218 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
219 <param name="isoform_rg" value="True" />
220 <output name="isoform_rg_output" ftype="tabular" file="isoform_rg.tabular" />
221 </test>
222 <test>
223 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
224 <param name="promoters_diff" value="True" />
225 <output name="promoters_diff_output" ftype="tabular" file="promoters_diff.tabular" />
226 </test>
227 <test>
228 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
229 <param name="read_groups" value="True" />
230 <output name="read_groups_output" ftype="tabular" file="read_groups.tabular" />
231 </test>
232 <test>
233 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
234 <param name="run_info" value="True" />
235 <output name="run_info_output" ftype="tabular" file="run_info.tabular" />
236 </test>
237 <test>
238 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
239 <param name="splicing_diff" value="True" />
240 <output name="splicing_diff_output" ftype="tabular" file="splicing_diff.tabular" />
241 </test>
242 <test>
243 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
244 <param name="tss_group_exp" value="True" />
245 <output name="tss_group_exp_output" ftype="tabular" file="tss_group_exp.tabular" />
246 </test>
247 <test>
248 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
249 <param name="tss_count_tracking" value="True" />
250 <output name="tss_count_tracking_output" ftype="tabular" file="tss_count_tracking.tabular" />
251 </test>
252 <test>
253 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
254 <param name="tss_fpkm" value="True" />
255 <output name="tss_fpkm_output" ftype="tabular" file="tss_fpkm.tabular" />
256 </test>
257 <test>
258 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
259 <param name="tss_rg" value="True" />
260 <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" />
261 </test>
262 <test>
263 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
264 <param name="var_model" value="True" />
265 <output name="var_model_output" ftype="tabular" file="var_model.tabular" />
266 </test>
267 </tests>
268 </tool>