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comparison cummerbund_to_tabular.xml @ 2:0761bbc0a4e7 draft default tip

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author devteam
date Thu, 02 Apr 2015 16:14:22 -0400
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1:36f917aa4b60 2:0761bbc0a4e7
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="cummerbund_to_cuffdiff" name="Extract CuffDiff" version="1.0.1"> 2 <tool id="cummerbund_to_cuffdiff" name="Extract CuffDiff" version="1.0.1">
3 <description>tabular files from a cummeRbund database</description> 3 <description>tabular files from a cummeRbund database</description>
4 <command interpreter="python"><![CDATA[ 4 <command interpreter="python"><![CDATA[
5 cummerbund_to_tabular.py --file ${input_database} 5 cummerbund_to_tabular.py --file ${input_database} ${' '.join(str($tables).split(','))}
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> 6 ]]></command>
12 <inputs> 7 <inputs>
13 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" /> 8 <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" /> 9 <param type="select" name="tables" multiple="True" label="Select tables to output">
15 <param type="boolean" name="cds_diff" truevalue="--tables cds_diff" falsevalue="" label="CDS overloading diffential expression testing" /> 10 <option name="cds_count" value="--tables cds_count">CDS count tracking</option>
16 <param type="boolean" name="cds_exp_diff" truevalue="--tables cds_exp_diff" falsevalue="" label="CDS FPKM differential expression testing" /> 11 <option name="cds_diff" value="--tables cds_diff">CDS overloading diffential expression testing</option>
17 <param type="boolean" name="cds_fpkm" truevalue="--tables cds_fpkm" falsevalue="" label="CDS FPKM tracking" /> 12 <option name="cds_exp_diff" value="--tables cds_exp_diff">CDS FPKM differential expression testing</option>
18 <param type="boolean" name="cds_rg" truevalue="--tables cds_rg" falsevalue="" label="CDS read groups" /> 13 <option name="cds_fpkm" value="--tables cds_fpkm">CDS FPKM tracking</option>
19 <param type="boolean" name="gene_exp_diff" truevalue="--tables gene_exp_diff" falsevalue="" label="gene differential expression testing" /> 14 <option name="cds_rg" value="--tables cds_rg">CDS read groups</option>
20 <param type="boolean" name="genes_count" truevalue="--tables genes_count" falsevalue="" label="gene count tracking" /> 15 <option name="gene_exp_diff" value="--tables gene_exp_diff">Gene differential expression testing</option>
21 <param type="boolean" name="genes_fpkm" truevalue="--tables genes_fpkm" falsevalue="" label="gene FPKM tracking" /> 16 <option name="genes_count" value="--tables genes_count">Gene count tracking</option>
22 <param type="boolean" name="gene_rg" truevalue="--tables gene_rg" falsevalue="" label="gene read groups" /> 17 <option name="genes_fpkm" value="--tables genes_fpkm">Gene FPKM tracking</option>
23 <param type="boolean" name="isoform_exp_diff" truevalue="--tables isoform_exp_diff" falsevalue="" label="transcript differential expression testing" /> 18 <option name="gene_rg" value="--tables gene_rg">Gene read groups</option>
24 <param type="boolean" name="isoform_count" truevalue="--tables isoform_count" falsevalue="" label="transcript count tracking" /> 19 <option name="isoform_exp_diff" value="--tables isoform_exp_diff">Transcript differential expression testing</option>
25 <param type="boolean" name="isoform_fpkm" truevalue="--tables isoform_fpkm" falsevalue="" label="transcript FPKM tracking" /> 20 <option name="isoform_count" value="--tables isoform_count">Transcript count tracking</option>
26 <param type="boolean" name="isoform_rg" truevalue="--tables isoform_rg" falsevalue="" label="transcript read groups" /> 21 <option name="isoform_fpkm" value="--tables isoform_fpkm">Transcript FPKM tracking</option>
27 <param type="boolean" name="promoters_diff" truevalue="--tables promoters_diff" falsevalue="" label="promoter differential testing" /> 22 <option name="isoform_rg" value="--tables isoform_rg">Transcript read groups</option>
28 <param type="boolean" name="read_groups" truevalue="--tables read_groups" falsevalue="" label="Read Groups" /> 23 <option name="promoters_diff" value="--tables promoters_diff">Promoter differential testing</option>
29 <param type="boolean" name="run_info" truevalue="--tables run_info" falsevalue="" label="Run details" /> 24 <option name="read_groups" value="--tables read_groups">Read Groups</option>
30 <param type="boolean" name="splicing_diff" truevalue="--tables splicing_diff" falsevalue="" label="splicing differential expression testing" /> 25 <option name="run_info" value="--tables run_info">Run details</option>
31 <param type="boolean" name="tss_group_exp" truevalue="--tables tss_group_exp" falsevalue="" label="TSS groups differential expression testing" /> 26 <option name="splicing_diff" value="--tables splicing_diff">Splicing differential expression testing</option>
32 <param type="boolean" name="tss_count_tracking" truevalue="--tables tss_count_tracking" falsevalue="" label="TSS count FPKM tracking" /> 27 <option name="tss_group_exp" value="--tables tss_group_exp">TSS groups differential expression testing</option>
33 <param type="boolean" name="tss_fpkm" truevalue="--tables tss_fpkm" falsevalue="" label="TSS groups FPKM tracking" /> 28 <option name="tss_count_tracking" value="--tables tss_count_tracking">TSS count FPKM tracking</option>
34 <param type="boolean" name="tss_rg" truevalue="--tables tss_rg" falsevalue="" label="TSS read groups" /> 29 <option name="tss_fpkm" value="--tables tss_fpkm">TSS groups FPKM tracking</option>
35 <param type="boolean" name="var_model" truevalue="--tables var_model" falsevalue="" label="var_model.info" /> 30 <option name="tss_rg" value="--tables tss_rg">TSS read groups</option>
31 <option name="var_model" value="--tables var_model">Model info</option>
32 </param>
36 </inputs> 33 </inputs>
37 <outputs> 34 <outputs>
38 <data format="tabular" name="cds_count_output" from_work_dir="cds_count.tabular" label="${tool.name} on ${on_string}: CDS count tracking"> 35 <data format="tabular" name="cds_count_output" from_work_dir="cds_count.tabular" label="${tool.name} on ${on_string}: CDS count tracking">
39 <filter>(cds_count is True)</filter> 36 <filter>('--tables cds_count' in tables)</filter>
40 </data> 37 </data>
41 <data format="tabular" name="cds_diff_output" from_work_dir="cds_diff.tabular" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing"> 38 <data format="tabular" name="cds_diff_output" from_work_dir="cds_diff.tabular" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
42 <filter>(cds_diff is True)</filter> 39 <filter>('--tables cds_diff' in tables)</filter>
43 </data> 40 </data>
44 <data format="tabular" name="cds_exp_diff_output" from_work_dir="cds_exp_diff.tabular" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing"> 41 <data format="tabular" name="cds_exp_diff_output" from_work_dir="cds_exp_diff.tabular" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing">
45 <filter>(cds_exp_diff is True)</filter> 42 <filter>('--tables cds_exp_diff' in tables)</filter>
46 </data> 43 </data>
47 <data format="tabular" name="cds_fpkm_output" from_work_dir="cds_fpkm.tabular" label="${tool.name} on ${on_string}: CDS FPKM tracking"> 44 <data format="tabular" name="cds_fpkm_output" from_work_dir="cds_fpkm.tabular" label="${tool.name} on ${on_string}: CDS FPKM tracking">
48 <filter>(cds_fpkm is True)</filter> 45 <filter>('--tables cds_fpkm' in tables)</filter>
49 </data> 46 </data>
50 <data format="tabular" name="cds_rg_output" from_work_dir="cds_rg.tabular" label="${tool.name} on ${on_string}: CDS read groups"> 47 <data format="tabular" name="cds_rg_output" from_work_dir="cds_rg.tabular" label="${tool.name} on ${on_string}: CDS read groups">
51 <filter>(cds_rg is True)</filter> 48 <filter>('--tables cds_rg' in tables)</filter>
52 </data> 49 </data>
53 <data format="tabular" name="gene_exp_diff_output" from_work_dir="gene_exp_diff.tabular" label="${tool.name} on ${on_string}: gene differential expression testing"> 50 <data format="tabular" name="gene_exp_diff_output" from_work_dir="gene_exp_diff.tabular" label="${tool.name} on ${on_string}: gene differential expression testing">
54 <filter>(gene_exp_diff is True)</filter> 51 <filter>('--tables gene_exp_diff' in tables)</filter>
55 </data> 52 </data>
56 <data format="tabular" name="genes_count_output" from_work_dir="genes_count.tabular" label="${tool.name} on ${on_string}: gene count tracking"> 53 <data format="tabular" name="genes_count_output" from_work_dir="genes_count.tabular" label="${tool.name} on ${on_string}: gene count tracking">
57 <filter>(genes_count is True)</filter> 54 <filter>('--tables genes_count' in tables)</filter>
58 </data> 55 </data>
59 <data format="tabular" name="genes_fpkm_output" from_work_dir="genes_fpkm.tabular" label="${tool.name} on ${on_string}: gene FPKM tracking"> 56 <data format="tabular" name="genes_fpkm_output" from_work_dir="genes_fpkm.tabular" label="${tool.name} on ${on_string}: gene FPKM tracking">
60 <filter>(genes_fpkm is True)</filter> 57 <filter>('--tables genes_fpkm' in tables)</filter>
61 </data> 58 </data>
62 <data format="tabular" name="gene_rg_output" from_work_dir="gene_rg.tabular" label="${tool.name} on ${on_string}: gene read groups"> 59 <data format="tabular" name="gene_rg_output" from_work_dir="gene_rg.tabular" label="${tool.name} on ${on_string}: gene read groups">
63 <filter>(gene_rg is True)</filter> 60 <filter>('--tables gene_rg' in tables)</filter>
64 </data> 61 </data>
65 <data format="tabular" name="isoform_exp_diff_output" from_work_dir="isoform_exp_diff.tabular" label="${tool.name} on ${on_string}: transcript differential expression testing"> 62 <data format="tabular" name="isoform_exp_diff_output" from_work_dir="isoform_exp_diff.tabular" label="${tool.name} on ${on_string}: transcript differential expression testing">
66 <filter>(isoform_exp_diff is True)</filter> 63 <filter>('--tables isoform_exp_diff' in tables)</filter>
67 </data> 64 </data>
68 <data format="tabular" name="isoform_count_output" from_work_dir="isoform_count.tabular" label="${tool.name} on ${on_string}: transcript count tracking"> 65 <data format="tabular" name="isoform_count_output" from_work_dir="isoform_count.tabular" label="${tool.name} on ${on_string}: transcript count tracking">
69 <filter>(isoform_count is True)</filter> 66 <filter>('--tables isoform_count' in tables)</filter>
70 </data> 67 </data>
71 <data format="tabular" name="isoform_fpkm_output" from_work_dir="isoform_fpkm.tabular" label="${tool.name} on ${on_string}: transcript FPKM tracking"> 68 <data format="tabular" name="isoform_fpkm_output" from_work_dir="isoform_fpkm.tabular" label="${tool.name} on ${on_string}: transcript FPKM tracking">
72 <filter>(isoform_fpkm is True)</filter> 69 <filter>('--tables isoform_fpkm' in tables)</filter>
73 </data> 70 </data>
74 <data format="tabular" name="isoform_rg_output" from_work_dir="isoform_rg.tabular" label="${tool.name} on ${on_string}: transcript read groups"> 71 <data format="tabular" name="isoform_rg_output" from_work_dir="isoform_rg.tabular" label="${tool.name} on ${on_string}: transcript read groups">
75 <filter>(isoform_rg is True)</filter> 72 <filter>('--tables isoform_rg' in tables)</filter>
76 </data> 73 </data>
77 <data format="tabular" name="promoters_diff_output" from_work_dir="promoters_diff.tabular" label="${tool.name} on ${on_string}: promoter differential testing"> 74 <data format="tabular" name="promoters_diff_output" from_work_dir="promoters_diff.tabular" label="${tool.name} on ${on_string}: promoter differential testing">
78 <filter>(promoters_diff is True)</filter> 75 <filter>('--tables promoters_diff' in tables)</filter>
79 </data> 76 </data>
80 <data format="tabular" name="read_groups_output" from_work_dir="read_groups.tabular" label="${tool.name} on ${on_string}: Read Groups"> 77 <data format="tabular" name="read_groups_output" from_work_dir="read_groups.tabular" label="${tool.name} on ${on_string}: Read Groups">
81 <filter>(read_groups is True)</filter> 78 <filter>('--tables read_groups' in tables)</filter>
82 </data> 79 </data>
83 <data format="tabular" name="run_info_output" from_work_dir="run_info.tabular" label="${tool.name} on ${on_string}: Run details"> 80 <data format="tabular" name="run_info_output" from_work_dir="run_info.tabular" label="${tool.name} on ${on_string}: Run details">
84 <filter>(run_info is True)</filter> 81 <filter>('--tables run_info' in tables)</filter>
85 </data> 82 </data>
86 <data format="tabular" name="splicing_diff_output" from_work_dir="splicing_diff.tabular" label="${tool.name} on ${on_string}: splicing differential expression testing"> 83 <data format="tabular" name="splicing_diff_output" from_work_dir="splicing_diff.tabular" label="${tool.name} on ${on_string}: splicing differential expression testing">
87 <filter>(splicing_diff is True)</filter> 84 <filter>('--tables splicing_diff' in tables)</filter>
88 </data> 85 </data>
89 <data format="tabular" name="tss_group_exp_output" from_work_dir="tss_group_exp.tabular" label="${tool.name} on ${on_string}: TSS groups differential expression testing"> 86 <data format="tabular" name="tss_group_exp_output" from_work_dir="tss_group_exp.tabular" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
90 <filter>(tss_group_exp is True)</filter> 87 <filter>('--tables tss_group_exp' in tables)</filter>
91 </data> 88 </data>
92 <data format="tabular" name="tss_count_tracking_output" from_work_dir="tss_count_tracking.tabular" label="${tool.name} on ${on_string}: TSS count FPKM tracking"> 89 <data format="tabular" name="tss_count_tracking_output" from_work_dir="tss_count_tracking.tabular" label="${tool.name} on ${on_string}: TSS count FPKM tracking">
93 <filter>(tss_count_tracking is True)</filter> 90 <filter>('--tables tss_count_tracking' in tables)</filter>
94 </data> 91 </data>
95 <data format="tabular" name="tss_fpkm_output" from_work_dir="tss_fpkm.tabular" label="${tool.name} on ${on_string}: TSS groups FPKM tracking"> 92 <data format="tabular" name="tss_fpkm_output" from_work_dir="tss_fpkm.tabular" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
96 <filter>(tss_fpkm is True)</filter> 93 <filter>('--tables tss_fpkm' in tables)</filter>
97 </data> 94 </data>
98 <data format="tabular" name="tss_rg_output" from_work_dir="tss_rg.tabular" label="${tool.name} on ${on_string}: TSS read groups"> 95 <data format="tabular" name="tss_rg_output" from_work_dir="tss_rg.tabular" label="${tool.name} on ${on_string}: TSS read groups">
99 <filter>(tss_rg is True)</filter> 96 <filter>('--tables tss_rg' in tables)</filter>
100 </data> 97 </data>
101 <data format="tabular" name="var_model_output" from_work_dir="var_model.tabular" label="${tool.name} on ${on_string}: var_model.info"> 98 <data format="tabular" name="var_model_output" from_work_dir="var_model.tabular" label="${tool.name} on ${on_string}: var_model.info">
102 <filter>(var_model is True)</filter> 99 <filter>('--tables var_model' in tables)</filter>
103 </data> 100 </data>
104 </outputs> 101 </outputs>
105 <citations> 102 <citations>
106 <citation type="doi">doi:10.1038/nprot.2012.016</citation> 103 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
107 </citations> 104 </citations>
108 <help>This tool extracts cuffdiff tabular files from a cummeRbund SQLite database.</help> 105 <help>This tool extracts cuffdiff tabular files from a cummeRbund SQLite database.</help>
109 <tests> 106 <tests>
110 <test> 107 <test>
111 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 108 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
112 <param name="cds_count" value="True" /> 109 <param name="tables" value="--tables cds_count,--tables cds_diff,--tables cds_exp_diff,--tables cds_fpkm,--tables cds_rg,--tables gene_exp_diff,--tables genes_count,--tables genes_fpkm,--tables gene_rg,--tables isoform_exp_diff,--tables isoform_count,--tables isoform_fpkm,--tables isoform_rg,--tables promoters_diff,--tables read_groups,--tables run_info,--tables splicing_diff,--tables tss_group_exp,--tables tss_count_tracking,--tables tss_fpkm,--tables tss_rg,--tables var_model" />
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" /> 110 <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" />
135 <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" /> 111 <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" /> 112 <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" /> 113 <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" />
138 <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" /> 114 <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" />
154 <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" /> 130 <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" />
155 <output name="var_model_output" ftype="tabular" file="var_model.tabular" /> 131 <output name="var_model_output" ftype="tabular" file="var_model.tabular" />
156 </test> 132 </test>
157 <test> 133 <test>
158 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 134 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
159 <param name="cds_count" value="True" /> 135 <param name="tables" value="--tables cds_count" />
160 <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" /> 136 <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" />
161 </test> 137 </test>
162 <test> 138 <test>
163 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 139 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
164 <param name="cds_diff" value="True" /> 140 <param name="tables" value="--tables cds_diff" />
165 <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" /> 141 <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" />
166 </test> 142 </test>
167 <test> 143 <test>
168 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 144 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
169 <param name="cds_exp_diff" value="True" /> 145 <param name="tables" value="--tables cds_exp_diff" />
170 <output name="cds_exp_diff_output" ftype="tabular" file="cds_exp_diff.tabular" /> 146 <output name="cds_exp_diff_output" ftype="tabular" file="cds_exp_diff.tabular" />
171 </test> 147 </test>
172 <test> 148 <test>
173 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 149 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
174 <param name="cds_fpkm" value="True" /> 150 <param name="tables" value="--tables cds_fpkm" />
175 <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" /> 151 <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" />
176 </test> 152 </test>
177 <test> 153 <test>
178 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 154 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
179 <param name="cds_rg" value="True" /> 155 <param name="tables" value="--tables cds_rg" />
180 <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" /> 156 <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" />
181 </test> 157 </test>
182 <test> 158 <test>
183 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 159 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
184 <param name="gene_exp_diff" value="True" /> 160 <param name="tables" value="--tables gene_exp_diff" />
185 <output name="gene_exp_diff_output" ftype="tabular" file="gene_exp_diff.tabular" /> 161 <output name="gene_exp_diff_output" ftype="tabular" file="gene_exp_diff.tabular" />
186 </test> 162 </test>
187 <test> 163 <test>
188 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 164 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
189 <param name="genes_count" value="True" /> 165 <param name="tables" value="--tables genes_count" />
190 <output name="genes_count_output" ftype="tabular" file="genes_count.tabular" /> 166 <output name="genes_count_output" ftype="tabular" file="genes_count.tabular" />
191 </test> 167 </test>
192 <test> 168 <test>
193 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 169 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
194 <param name="genes_fpkm" value="True" /> 170 <param name="tables" value="--tables genes_fpkm" />
195 <output name="genes_fpkm_output" ftype="tabular" file="genes_fpkm.tabular" /> 171 <output name="genes_fpkm_output" ftype="tabular" file="genes_fpkm.tabular" />
196 </test> 172 </test>
197 <test> 173 <test>
198 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 174 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
199 <param name="gene_rg" value="True" /> 175 <param name="tables" value="--tables gene_rg" />
200 <output name="gene_rg_output" ftype="tabular" file="gene_rg.tabular" /> 176 <output name="gene_rg_output" ftype="tabular" file="gene_rg.tabular" />
201 </test> 177 </test>
202 <test> 178 <test>
203 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 179 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
204 <param name="isoform_exp_diff" value="True" /> 180 <param name="tables" value="--tables isoform_exp_diff" />
205 <output name="isoform_exp_diff_output" ftype="tabular" file="isoform_exp_diff.tabular" /> 181 <output name="isoform_exp_diff_output" ftype="tabular" file="isoform_exp_diff.tabular" />
206 </test> 182 </test>
207 <test> 183 <test>
208 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 184 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
209 <param name="isoform_count" value="True" /> 185 <param name="tables" value="--tables isoform_count" />
210 <output name="isoform_count_output" ftype="tabular" file="isoform_count.tabular" /> 186 <output name="isoform_count_output" ftype="tabular" file="isoform_count.tabular" />
211 </test> 187 </test>
212 <test> 188 <test>
213 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 189 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
214 <param name="isoform_fpkm" value="True" /> 190 <param name="tables" value="--tables isoform_fpkm" />
215 <output name="isoform_fpkm_output" ftype="tabular" file="isoform_fpkm.tabular" /> 191 <output name="isoform_fpkm_output" ftype="tabular" file="isoform_fpkm.tabular" />
216 </test> 192 </test>
217 <test> 193 <test>
218 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 194 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
219 <param name="isoform_rg" value="True" /> 195 <param name="tables" value="--tables isoform_rg" />
220 <output name="isoform_rg_output" ftype="tabular" file="isoform_rg.tabular" /> 196 <output name="isoform_rg_output" ftype="tabular" file="isoform_rg.tabular" />
221 </test> 197 </test>
222 <test> 198 <test>
223 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 199 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
224 <param name="promoters_diff" value="True" /> 200 <param name="tables" value="--tables promoters_diff" />
225 <output name="promoters_diff_output" ftype="tabular" file="promoters_diff.tabular" /> 201 <output name="promoters_diff_output" ftype="tabular" file="promoters_diff.tabular" />
226 </test> 202 </test>
227 <test> 203 <test>
228 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 204 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
229 <param name="read_groups" value="True" /> 205 <param name="tables" value="--tables read_groups" />
230 <output name="read_groups_output" ftype="tabular" file="read_groups.tabular" /> 206 <output name="read_groups_output" ftype="tabular" file="read_groups.tabular" />
231 </test> 207 </test>
232 <test> 208 <test>
233 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 209 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
234 <param name="run_info" value="True" /> 210 <param name="tables" value="--tables run_info" />
235 <output name="run_info_output" ftype="tabular" file="run_info.tabular" /> 211 <output name="run_info_output" ftype="tabular" file="run_info.tabular" />
236 </test> 212 </test>
237 <test> 213 <test>
238 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 214 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
239 <param name="splicing_diff" value="True" /> 215 <param name="tables" value="--tables splicing_diff" />
240 <output name="splicing_diff_output" ftype="tabular" file="splicing_diff.tabular" /> 216 <output name="splicing_diff_output" ftype="tabular" file="splicing_diff.tabular" />
241 </test> 217 </test>
242 <test> 218 <test>
243 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 219 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
244 <param name="tss_group_exp" value="True" /> 220 <param name="tables" value="--tables tss_group_exp" />
245 <output name="tss_group_exp_output" ftype="tabular" file="tss_group_exp.tabular" /> 221 <output name="tss_group_exp_output" ftype="tabular" file="tss_group_exp.tabular" />
246 </test> 222 </test>
247 <test> 223 <test>
248 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 224 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
249 <param name="tss_count_tracking" value="True" /> 225 <param name="tables" value="--tables tss_count_tracking" />
250 <output name="tss_count_tracking_output" ftype="tabular" file="tss_count_tracking.tabular" /> 226 <output name="tss_count_tracking_output" ftype="tabular" file="tss_count_tracking.tabular" />
251 </test> 227 </test>
252 <test> 228 <test>
253 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 229 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
254 <param name="tss_fpkm" value="True" /> 230 <param name="tables" value="--tables tss_fpkm" />
255 <output name="tss_fpkm_output" ftype="tabular" file="tss_fpkm.tabular" /> 231 <output name="tss_fpkm_output" ftype="tabular" file="tss_fpkm.tabular" />
256 </test> 232 </test>
257 <test> 233 <test>
258 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 234 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
259 <param name="tss_rg" value="True" /> 235 <param name="tables" value="--tables tss_rg" />
260 <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" /> 236 <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" />
261 </test> 237 </test>
262 <test> 238 <test>
263 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" /> 239 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
264 <param name="var_model" value="True" /> 240 <param name="tables" value="--tables var_model" />
265 <output name="var_model_output" ftype="tabular" file="var_model.tabular" /> 241 <output name="var_model_output" ftype="tabular" file="var_model.tabular" />
266 </test> 242 </test>
267 </tests> 243 </tests>
268 </tool> 244 </tool>