Mercurial > repos > jjohnson > cummerbund

annotate cuffdiff_wrapper.xml @ 14:d10befb0867a

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add library_norm_method and dispersion_method params to cuffdiff tool.
author Jim Johnson <jj@umn.edu>
date Wed, 17 Jul 2013 08:25:52 -0500
parents 4597c429b6fb
children 2d7eee38ab5b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
4597c429b6fb Return nonzero exit code from cuffdiff_wrapper.py on error
Jim Johnson <jj@umn.edu>
parents: 11
diff changeset
1 <tool id="cuffdiff_cummerbund" name="Cuffdiff" 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>find significant changes in transcript expression, splicing, and promoter use</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 interpreter="python">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
8 #set sel_outputs = $output_sel.__str__.split(',')
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
9 cuffdiff_wrapper.py
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
10 --FDR=$fdr
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
11 --num-threads="4"
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
12 --min-alignment-count=$min_alignment_count
14
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
13 --library-norm-method=$library_norm_method
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
14 --dispersion-method=$dispersion_method
1
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 'cuffdata' in $sel_outputs or not $output_sel:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
17 --cuffdatadir=$cuffdata.extra_files_path
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 'cummeRbund_db' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
20 --cummeRbund_db=$cummeRbund_db
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 'isoforms_fpkm_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
24 --isoforms_fpkm_tracking_output=$isoforms_fpkm_tracking
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 'genes_fpkm_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
27 --genes_fpkm_tracking_output=$genes_fpkm_tracking
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 $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
30 --cds_fpkm_tracking_output=$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 'tss_groups_fpkm_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
33 --tss_groups_fpkm_tracking_output=$tss_groups_fpkm_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 'isoforms_exp_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
36 --isoforms_exp_output=$isoforms_exp_diff
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 #if 'genes_exp_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
39 --genes_exp_output=$genes_exp_diff
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
40 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
41 #if 'tss_groups_exp_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
42 --tss_groups_exp_output=$tss_groups_exp_diff
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
43 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
44 #if 'cds_exp_fpkm_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
45 --cds_exp_fpkm_tracking_output=$cds_exp_fpkm_tracking
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
46 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
47 #if 'splicing_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
48 --splicing_diff_output=$splicing_diff
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
49 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
50 #if 'cds_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
51 --cds_diff_output=$cds_diff
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
52 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
53 #if 'promoters_diff' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
54 --promoters_diff_output=$promoters_diff
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
55 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
56 #if 'cds_read_group_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
57 --cds_read_group_tracking=$cds_read_group_tracking
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
58 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
59 #if 'tss_groups_read_group_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
60 --tss_groups_read_group_tracking=$tss_groups_read_group_tracking
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
61 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
62 #if 'genes_read_group_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
63 --genes_read_group_tracking=$genes_read_group_tracking
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
64 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
65 #if 'isoforms_read_group_tracking' in $sel_outputs:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
66 --isoforms_read_group_tracking=$isoforms_read_group_tracking
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
67 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
68
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
69 ## Set advanced data parameters?
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
70 #if $additional.sAdditional == "Yes":
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
71 -m $additional.frag_mean_len
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
72 -s $additional.frag_len_std_dev
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
73 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
74
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
75 ## Normalization?
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
76 #if str($do_normalization) == "Yes":
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
77 -N
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
78 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
79
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
80 ## Multi-read correct?
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
81 #if str($multiread_correct) == "Yes":
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
82 -u
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
83 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
84
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
85 ## Bias correction?
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
86 #if $bias_correction.do_bias_correction == "Yes":
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
87 -b
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
88 #if $bias_correction.seq_source.index_source == "history":
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
89 --ref_file=$bias_correction.seq_source.ref_file
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
90 #else:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
91 --ref_file="None"
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
92 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
93 --dbkey=${gtf_input.metadata.dbkey}
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
94 --index_dir=${GALAXY_DATA_INDEX_DIR}
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
95 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
96
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
97 ## Inputs.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
98 --inputA=$gtf_input
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
99 #if $group_analysis.do_groups == "No":
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
100 --input1=$aligned_reads1
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
101 --input2=$aligned_reads2
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
102 #else:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
103 ## Replicates.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
104 --labels
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
105 #for $group in $group_analysis.groups
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
106 ${group.group}
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
107 #end for
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
108 --files
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
109 #for $group in $group_analysis.groups
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
110 #for $file in $group.files:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
111 ${file.file}
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
112 #end for
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
113 ,
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
114 #end for
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
115 #end if
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
116
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
117 </command>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
118 <inputs>
13
4597c429b6fb Return nonzero exit code from cuffdiff_wrapper.py on error
Jim Johnson <jj@umn.edu>
parents: 11
diff changeset
119 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>
1
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
120 <conditional name="group_analysis">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
121 <param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group.">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
122 <option value="No">No</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
123 <option value="Yes">Yes</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
124 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
125 <when value="Yes">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
126 <repeat name="groups" title="Group">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
127 <param name="group" title="Group name" type="text" label="Group name (no spaces or commas)"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
128 <repeat name="files" title="Replicate">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
129 <param name="file" label="Add file" type="data" format="sam,bam"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
130 </repeat>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
131 </repeat>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
132 </when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
133 <when value="No">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
134 <param format="sam,bam" name="aligned_reads1" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
135 <param format="sam,bam" name="aligned_reads2" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
136 </when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
137 </conditional>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
138
14
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
139 <param name="library_norm_method" type="select" label="Library normalization method">
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
140 <option value="geometric" selected="True">geometric</option>
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
141 <option value="classic-fpkm">classic-fpkm</option>
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
142 <option value="quartile">quartile</option>
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
143 </param>
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
144
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
145 <param name="dispersion_method" type="select" label="Dispersion estimation method" help="If using only one sample per condition, you must use 'blind.'">
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
146 <option value="pooled" selected="True">pooled</option>
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
147 <option value="per-condition">per-condition</option>
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
148 <option value="blind">blind</option>
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
149 </param>
d10befb0867a Add library_norm_method and dispersion_method params to cuffdiff tool.
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
150
1
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
151 <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
152
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
153 <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
154
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
155 <param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts.">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
156 <option value="No">No</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
157 <option value="Yes">Yes</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
158 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
159
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
160 <param name="multiread_correct" type="select" label="Use multi-read correct" help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
161 <option value="No" selected="true">No</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
162 <option value="Yes">Yes</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
163 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
164
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
165 <conditional name="bias_correction">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
166 <param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates.">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
167 <option value="No">No</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
168 <option value="Yes">Yes</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
169 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
170 <when value="Yes">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
171 <conditional name="seq_source">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
172 <param name="index_source" type="select" label="Reference sequence data">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
173 <option value="cached">Locally cached</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
174 <option value="history">History</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
175 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
176 <when value="cached"></when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
177 <when value="history">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
178 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
179 </when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
180 </conditional>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
181 </when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
182 <when value="No"></when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
183 </conditional>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
184
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
185 <conditional name="additional">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
186 <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended)">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
187 <option value="No">No</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
188 <option value="Yes">Yes</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
189 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
190 <when value="No"></when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
191 <when value="Yes">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
192 <param name="frag_mean_len" type="integer" value="200" label="Average Fragment Length"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
193 <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
194 </when>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
195 </conditional>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
196
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
197 <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
198 <option value="cuffdata">cuffdata - html page with links to cuffdiff outputs</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
199 <option value="cummeRbund_db">cummeRbund database</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
200 <option value="run_info">run.info</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
201 <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
202 <option value="splicing_diff">splicing.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
203 <option value="promoters_diff">promoters.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
204 <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
205 <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
206 <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
207 <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
208 <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
209 <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
210 <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
211 <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
212 <option value="cds_diff">cds.diff</option>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
213 <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
214 <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
215 <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
216 <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
217 <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
218 <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
219 <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
220 <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
221 </param>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
222
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
223 </inputs>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
224
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
225 <outputs>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
226 <data format="text" name="run_info" label="${tool.name} on ${on_string}: run.info">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
227 <filter>output_sel and 'run_info' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
228 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
229 <data format="tabular" name="read_groups_info" label="${tool.name} on ${on_string}: read_groups.info">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
230 <filter>output_sel and 'read_groups_info' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
231 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
232 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
233 <filter>output_sel and 'splicing_diff' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
234 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
235 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
236 <filter>output_sel and 'promoters_diff' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
237 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
238 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
239 <filter>output_sel and 'cds_diff' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
240 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
241 <data format="tabular" name="cds_exp_diff" label="${tool.name} on ${on_string}: CDS differential expression testing">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
242 <filter>output_sel and 'cds_exp_diff' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
243 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
244 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
245 <filter>output_sel and 'cds_fpkm_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
246 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
247 <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS counts">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
248 <filter>output_sel and 'cds_count_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
249 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
250 <data format="tabular" name="cds_read_group_tracking" label="${tool.name} on ${on_string}: CDS Read Group tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
251 <filter>output_sel and 'cds_read_group_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
252 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
253 <data format="tabular" name="tss_groups_exp_diff" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
2
de024d31e777 Correct exp_diff names
Jim Johnson <jj@umn.edu>
parents: 1
diff changeset
254 <filter>output_sel and 'tss_groups_exp_diff' in output_sel</filter>
1
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
255 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
256 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
257 <filter>output_sel and 'tss_groups_fpkm_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
258 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
259 <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS groups counts">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
260 <filter>output_sel and 'tss_groups_count_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
261 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
262 <data format="tabular" name="tss_groups_read_group_tracking" label="${tool.name} on ${on_string}: TSS groups Read Group tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
263 <filter>output_sel and 'tss_groups_read_group_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
264 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
265 <data format="tabular" name="isoforms_exp_diff" label="${tool.name} on ${on_string}: transcript differential expression testing">
2
de024d31e777 Correct exp_diff names
Jim Johnson <jj@umn.edu>
parents: 1
diff changeset
266 <filter>output_sel and 'isoforms_exp_diff' in output_sel</filter>
1
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
267 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
268 <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
269 <filter>output_sel and 'isoforms_fpkm_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
270 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
271 <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript counts">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
272 <filter>output_sel and 'isoforms_count_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
273 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
274 <data format="tabular" name="isoforms_read_group_tracking" label="${tool.name} on ${on_string}: transcript Read Group tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
275 <filter>output_sel and 'isoforms_read_group_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
276 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
277 <data format="tabular" name="genes_exp_diff" label="${tool.name} on ${on_string}: gene differential expression testing">
2
de024d31e777 Correct exp_diff names
Jim Johnson <jj@umn.edu>
parents: 1
diff changeset
278 <filter>output_sel and 'genes_exp_diff' in output_sel</filter>
1
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
279 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
280 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
281 <filter>output_sel and 'genes_fpkm_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
282 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
283 <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene counts">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
284 <filter>output_sel and 'genes_count_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
285 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
286 <data format="tabular" name="genes_read_group_tracking" label="${tool.name} on ${on_string}: gene Read Group tracking">
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
287 <filter>output_sel and 'genes_read_group_tracking' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
288 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
289 <data format="cuffdata" name="cuffdata" label="${tool.name} on ${on_string}: cuffdata" >
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
290 <filter>not output_sel or output_sel and 'cuffdata' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
291 </data>
6
79c687de829b Add more descriptive label
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
292 <data format="cuffdatadb" name="cummeRbund_db" label="${tool.name} on ${on_string}: cummeRbund sqlite Database" >
1
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
293 <filter>output_sel and 'cummeRbund_db' in output_sel</filter>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
294 </data>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
295 </outputs>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
296 <stdio>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
297 <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
298 </stdio>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
299
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
300
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
301 <tests>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
302 <test>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
303 <!--
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
304 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
305 -->
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
306 <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" />
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
307 <param name="do_groups" value="No" />
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
308 <param name="aligned_reads1" value="cuffdiff_in1.sam" ftype="sam" />
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
309 <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" />
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
310 <!-- Defaults. -->
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
311 <param name="fdr" value="0.05" />
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
312 <param name="min_alignment_count" value="0" />
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
313 <param name="do_bias_correction" value="No" />
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
314 <param name="do_normalization" value="No" />
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
315 <param name="multiread_correct" value="No"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
316 <param name="sAdditional" value="No"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
317 <!--
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
318 Line diffs are needed because cuffdiff does not produce deterministic output.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
319 TODO: can we find datasets that lead to deterministic behavior?
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
320 -->
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
321 <output name="splicing_diff" file="cuffdiff_out9.txt"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
322 <output name="promoters_diff" file="cuffdiff_out10.txt"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
323 <output name="cds_diff" file="cuffdiff_out11.txt"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
324 <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
325 <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
326 <output name="tss_groups_exp" file="cuffdiff_out3.txt" lines_diff="200"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
327 <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
328 <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
329 <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
330 <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
331 <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
332 </test>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
333 </tests>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
334
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
335 <help>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
336 **Cuffdiff Overview**
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
337
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
338 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
339
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
340 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
341
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
342 ------
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
343
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
344 **Know what you are doing**
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
345
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
346 .. class:: warningmark
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
347
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
348 There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
349
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
350 .. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
351
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
352 ------
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
353
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
354 **Input format**
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
355
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
356 Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
357
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
358 ------
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
359
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
360 **Outputs**
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
361
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
362 Cuffdiff produces many output files:
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
363
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
364 1. Transcript FPKM expression tracking.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
365 2. Gene FPKM expression tracking; tracks the summed FPKM of transcripts sharing each gene_id
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
366 3. Primary transcript FPKM tracking; tracks the summed FPKM of transcripts sharing each tss_id
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
367 4. Coding sequence FPKM tracking; tracks the summed FPKM of transcripts sharing each p_id, independent of tss_id
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
368 5. Transcript differential FPKM.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
369 6. Gene differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each gene_id
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
370 7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
371 8. Coding sequence differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each p_id independent of tss_id
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
372 9. Differential splicing tests: this tab delimited file lists, for each primary transcript, the amount of overloading detected among its isoforms, i.e. how much differential splicing exists between isoforms processed from a single primary transcript. Only primary transcripts from which two or more isoforms are spliced are listed in this file.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
373 10. Differential promoter tests: this tab delimited file lists, for each gene, the amount of overloading detected among its primary transcripts, i.e. how much differential promoter use exists between samples. Only genes producing two or more distinct primary transcripts (i.e. multi-promoter genes) are listed here.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
374 11. Differential CDS tests: this tab delimited file lists, for each gene, the amount of overloading detected among its coding sequences, i.e. how much differential CDS output exists between samples. Only genes producing two or more distinct CDS (i.e. multi-protein genes) are listed here.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
375
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
376 -------
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
377
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
378 **Settings**
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
379
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
380 All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
381
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
382 ------
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
383
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
384 **Cuffdiff parameter list**
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
385
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
386 This is a list of implemented Cuffdiff options::
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
387
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
388 -m INT Average fragement length; default 200
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
389 -s INT Fragment legnth standard deviation; default 80
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
390 -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
391 --FDR FLOAT The allowed false discovery rate. The default is 0.05.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
392 --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
393 --max-mle-iterations INT Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
394 -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts.
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
395
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
396 </help>
6a9bc26ab8d9 Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs
Jim Johnson <jj@umn.edu>
parents:
diff changeset
397 </tool>