Mercurial > repos > jjohnson > cummerbund

annotate cuffdata_datasets.xml @ 16:a29a35968ddb default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix tool_dependencies.xml
author Jim Johnson <jj@umn.edu>
date Fri, 08 Nov 2013 13:37:14 -0600
parents 9d25b0fd882b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
9d25b0fd882b Add cuffdatadb datatype (cummeRbund SQLite DB) to cuffdata.py
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
1 <tool id="cuffdata_datasets" name="Cuffdata datasets" version="0.0.6">
1
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
2 <!-- Wrapper supports Cuffdiff versions v1.3.0-v2.0 -->
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
3 <description>history datasets from Cuffdiff output</description>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
4 <requirements>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
5 <requirement type="package">cufflinks</requirement>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
6 </requirements>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
7 <command>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
8 #set sel_outputs = $output_sel.__str__.split(',')
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
9 #if 'run_info' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
10 cat ${cuffdata.extra_files_path}/run.info > $run_info;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
11 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
12 #if 'read_groups_info' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
13 cat ${cuffdata.extra_files_path}/read_groups.info > $read_groups_info;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
14 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
15
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
16 #if 'splicing_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
17 cat ${cuffdata.extra_files_path}/splicing.diff > $splicing_diff;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
18 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
19 #if 'promoters_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
20 cat ${cuffdata.extra_files_path}/promoters.diff > $promoters_diff;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
21 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
22
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
23 #if 'cds_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
24 cat ${cuffdata.extra_files_path}/cds.diff > $cds_diff;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
25 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
26 #if 'cds_exp_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
27 cat ${cuffdata.extra_files_path}/cds_exp.diff > $cds_exp_diff;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
28 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
29 #if 'cds_fpkm_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
30 cat ${cuffdata.extra_files_path}/cds.fpkm_tracking > $cds_fpkm_tracking;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
31 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
32 #if 'cds_count_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
33 cat ${cuffdata.extra_files_path}/cds.count_tracking > $cds_count_tracking;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
34 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
35 #if 'cds_read_group_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
36 cat ${cuffdata.extra_files_path}/cds.read_group_tracking > $cds_read_group_tracking;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
37 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
38
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
39 #if 'tss_groups_exp_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
40 cat ${cuffdata.extra_files_path}/tss_groups_exp.diff > $tss_groups_exp_diff;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
41 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
42 #if 'tss_groups_fpkm_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
43 cat ${cuffdata.extra_files_path}/tss_groups.fpkm_tracking > $tss_groups_fpkm_tracking;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
44 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
45 #if 'tss_groups_count_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
46 cat ${cuffdata.extra_files_path}/tss_groups.count_tracking > $tss_groups_count_tracking;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
47 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
48 #if 'tss_groups_read_group_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
49 cat ${cuffdata.extra_files_path}/tss_groups.read_group_tracking > $tss_groups_read_group_tracking;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
50 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
51
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
52 #if 'genes_exp_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
53 cat ${cuffdata.extra_files_path}/genes_exp.diff > $genes_exp_diff;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
54 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
55 #if 'genes_fpkm_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
56 cat ${cuffdata.extra_files_path}/genes.fpkm_tracking > $genes_fpkm_tracking;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
57 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
58 #if 'genes_count_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
59 cat ${cuffdata.extra_files_path}/genes.count_tracking > $genes_count_tracking;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
60 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
61 #if 'genes_read_group_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
62 cat ${cuffdata.extra_files_path}/genes.read_group_tracking > $genes_read_group_tracking;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
63 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
64
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
65 #if 'isoforms_exp_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
66 cat ${cuffdata.extra_files_path}/isoforms_exp.diff > $isoforms_exp_diff;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
67 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
68 #if 'isoforms_fpkm_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
69 cat ${cuffdata.extra_files_path}/isoforms.fpkm_tracking > $isoforms_fpkm_tracking;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
70 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
71 #if 'isoforms_count_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
72 cat ${cuffdata.extra_files_path}/isoforms.count_tracking > $isoforms_count_tracking;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
73 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
74 #if 'isoforms_read_group_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
75 cat ${cuffdata.extra_files_path}/isoforms.read_group_tracking > $isoforms_read_group_tracking;
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
76 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
77
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
78 </command>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
79 <inputs>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
80 <param name="cuffdata" type="data" format="cuffdata" label="Cuffidif cuffdata" help=""/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
81 <param name="output_sel" type="select" multiple="true" display="checkboxes" force_select="true" label="Select outputs for history datasets">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
82 <option value="run_info">run.info</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
83 <option value="read_groups_info">read_groups.info</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
84 <option value="splicing_diff">splicing.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
85 <option value="promoters_diff">promoters.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
86 <option value="genes_exp_diff">genes_exp.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
87 <option value="genes_fpkm_tracking">genes.fpkm_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
88 <option value="genes_count_tracking">genes.count_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
89 <option value="genes_read_group_tracking">genes.read_group_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
90 <option value="isoforms_exp_diff">isoforms.exp_diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
91 <option value="isoforms_fpkm_tracking">isoforms.fpkm_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
92 <option value="isoforms_count_tracking">isoforms.count_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
93 <option value="isoforms_read_group_tracking">isoforms.read_group_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
94 <option value="cds_diff">cds.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
95 <option value="cds_exp_diff">cds_exp.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
96 <option value="cds_fpkm_tracking">cds.fpkm_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
97 <option value="cds_count_tracking">cds.count_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
98 <option value="cds_read_group_tracking">cds.read_group_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
99 <option value="tss_groups_exp_diff">tss_groups_exp.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
100 <option value="tss_groups_fpkm_tracking">tss_groups.fpkm_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
101 <option value="tss_groups_count_tracking">tss_groups.count_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
102 <option value="tss_groups_read_group_tracking">tss_groups.read_group_tracking</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
103 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
104 </inputs>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
105
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
106 <outputs>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
107 <data format="text" name="run_info" label="${tool.name} on ${on_string}: run.info">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
108 <filter>'run_info' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
109 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
110 <data format="tabular" name="read_groups_info" label="${tool.name} on ${on_string}: read_groups.info">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
111 <filter>'read_groups_info' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
112 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
113 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
114 <filter>'splicing_diff' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
115 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
116 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
117 <filter>'promoters_diff' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
118 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
119 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
120 <filter>'cds_diff' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
121 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
122 <data format="tabular" name="cds_exp_diff" label="${tool.name} on ${on_string}: CDS differential expression testing">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
123 <filter>'cds_exp_diff' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
124 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
125 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
126 <filter>'cds_fpkm_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
127 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
128 <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS counts">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
129 <filter>'cds_count_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
130 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
131 <data format="tabular" name="cds_read_group_tracking" label="${tool.name} on ${on_string}: CDS Read Group tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
132 <filter>'cds_read_group_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
133 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
134 <data format="tabular" name="tss_groups_exp_diff" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
2
de024d31e777 Correct exp_diff names
Jim Johnson <jj@umn.edu>
parents: 1
diff changeset
135 <filter>'tss_groups_exp_diff' in output_sel</filter>
1
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
136 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
137 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
138 <filter>'tss_groups_fpkm_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
139 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
140 <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS groups counts">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
141 <filter>'tss_groups_count_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
142 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
143 <data format="tabular" name="tss_groups_read_group_tracking" label="${tool.name} on ${on_string}: TSS groups Read Group tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
144 <filter>'tss_groups_read_group_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
145 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
146 <data format="tabular" name="isoforms_exp_diff" label="${tool.name} on ${on_string}: transcript differential expression testing">
2
de024d31e777 Correct exp_diff names
Jim Johnson <jj@umn.edu>
parents: 1
diff changeset
147 <filter>'isoforms_exp_diff' in output_sel</filter>
1
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
148 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
149 <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
150 <filter>'isoforms_fpkm_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
151 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
152 <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript counts">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
153 <filter>'isoforms_count_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
154 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
155 <data format="tabular" name="isoforms_read_group_tracking" label="${tool.name} on ${on_string}: transcript Read Group tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
156 <filter>'isoforms_read_group_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
157 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
158 <data format="tabular" name="genes_exp_diff" label="${tool.name} on ${on_string}: gene differential expression testing">
2
de024d31e777 Correct exp_diff names
Jim Johnson <jj@umn.edu>
parents: 1
diff changeset
159 <filter>'genes_exp_diff' in output_sel</filter>
1
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
160 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
161 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
162 <filter>'genes_fpkm_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
163 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
164 <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene counts">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
165 <filter>'genes_count_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
166 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
167 <data format="tabular" name="genes_read_group_tracking" label="${tool.name} on ${on_string}: gene Read Group tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
168 <filter>'genes_read_group_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
169 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
170 </outputs>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
171 <stdio>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
172 <exit_code range="1:" level="fatal" description="Cufflinks Err" />
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
173 </stdio>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
174
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
175
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
176 <tests>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
177 </tests>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
178
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
179 <help>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
180 **Cuffdata to history datasets**
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
181
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
182 Copy Cuffdiff output files from a cuffdata html page to datasets in your history.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
183
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
184 Cuffdiff is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
185
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
186 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
187
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
188 </help>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
189 </tool>