Mercurial > repos > devteam > cufflinks

annotate cufflinks_wrapper.xml @ 11:e04dbae2abe0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
author devteam
date Sun, 19 Feb 2017 12:12:28 -0500
parents 83bec71c5c9f
children d080005cffe1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
e04dbae2abe0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
devteam
parents: 10
diff changeset
1 <tool id="cufflinks" name="Cufflinks" version="@VERSION@.2">
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
2 <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description>
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
3 <macros>
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
4 <import>cuff_macros.xml</import>
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
5 </macros>
11
e04dbae2abe0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
devteam
parents: 10
diff changeset
6 <expand macro="requirements" />
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
7 <version_command>cufflinks 2>&amp;1 | head -n 1</version_command>
11
e04dbae2abe0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
devteam
parents: 10
diff changeset
8 <command detect_errors="aggressive">
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
9 python '$__tool_directory__/cufflinks_wrapper.py'
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
10 --input '$input'
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
11 --assembled-isoforms-output '$assembled_isoforms'
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
12 --num-threads "\${GALAXY_SLOTS:-4}"
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
13 -I $max_intron_len
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
14 -F $min_isoform_fraction
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
15 -j $pre_mrna_fraction
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
16 $length_correction
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
17
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
18 ## Include reference annotation?
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
19 #if $reference_annotation.use_ref == "Use reference annotation":
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
20 -G '$reference_annotation.reference_annotation_file'
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
21 $reference_annotation.compatible_hits_norm
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
22 #end if
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
23 #if $reference_annotation.use_ref == "Use reference annotation guide":
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
24 -g '$reference_annotation.reference_annotation_guide_file'
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
25 --3-overhang-tolerance $reference_annotation.three_overhang_tolerance
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
26 --intron-overhang-tolerance $reference_annotation.intron_overhang_tolerance
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
27 $reference_annotation.no_faux_reads
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
28 #end if
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
29
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
30 ## Bias correction?
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
31 #if $bias_correction.do_bias_correction == "Yes":
2
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents: 0
diff changeset
32 -b
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
33 #if $bias_correction.seq_source.index_source == "history":
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
34 --ref_file '$bias_correction.seq_source.ref_file'
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
35 #else:
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
36 --index '${bias_correction.seq_source.index.fields.path}'
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
37 #end if
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
38 #end if
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
39
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
40 ## Multi-read correct?
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
41 #if str($multiread_correct) == "Yes":
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
42 -u
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
43 #end if
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
44
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
45 ## Include global model if available.
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
46 #if $global_model:
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
47 --global_model '$global_model'
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
48 #end if
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
49
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
50 ## advanced settings
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
51 #if $advanced_settings.use_advanced_settings == "Yes":
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
52 --library-type $advanced_settings.library_type
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
53 #if $advanced_settings.mask_file:
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
54 --mask-file '$advanced_settings.mask_file'
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
55 #end if
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
56 --inner-mean-dist $advanced_settings.inner_mean_dist
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
57 --inner-dist-std-dev $advanced_settings.inner_dist_std_dev
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
58 --max-mle-iterations $advanced_settings.max_mle_iterations
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
59 --junc-alpha $advanced_settings.junc_alpha
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
60 --small-anchor-fraction $advanced_settings.small_anchor_fraction
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
61 --overhang-tolerance $advanced_settings.overhang_tolerance
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
62 --max-bundle-length $advanced_settings.max_bundle_length
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
63 --max-bundle-frags $advanced_settings.max_bundle_frags
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
64 --min-intron-length $advanced_settings.min_intron_length
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
65 --trim-3-avgcov-thresh $advanced_settings.trim_three_avgcov_thresh
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
66 --trim-3-dropoff-frac $advanced_settings.trim_three_dropoff_frac
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
67 #end if
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
68 </command>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
69 <inputs>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
70 <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
71 <param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help="ignore alignments with gaps longer than this"/>
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
72 <param name="min_isoform_fraction" type="float" value="0.10" min="0" max="1" label="Min Isoform Fraction" help="suppress transcripts below this abundance level"/>
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
73 <param name="pre_mrna_fraction" type="float" value="0.15" min="0" max="1" label="Pre MRNA Fraction" help="suppress intra-intronic transcripts below this level"/>
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
74 <conditional name="reference_annotation">
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
75 <param name="use_ref" type="select" label="Use Reference Annotation">
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
76 <option value="No" selected="true">No</option>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
77 <option value="Use reference annotation">Use reference annotation</option>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
78 <option value="Use reference annotation guide">Use reference annotation as guide</option>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
79 </param>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
80 <when value="No" />
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
81 <when value="Use reference annotation">
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
82 <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
83 <param name="compatible_hits_norm" type="select" label="Count hits compatible with reference RNAs only"
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
84 help="With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped hits used in the FPKM denominator. This option can only be used in combination with --GTF.">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
85 <option value="" selected="True">No</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
86 <option value="--compatible-hits-norm">Yes</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
87 </param>
2
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents: 0
diff changeset
88 </when>
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents: 0
diff changeset
89 <when value="Use reference annotation guide">
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
90 <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
91 <param name="three_overhang_tolerance" type="integer" value="600" label="3prime overhang tolerance"
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
92 help="The number of bp allowed to overhang the 3prime end of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 600 bp." />
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
93 <param name="intron_overhang_tolerance" type="integer" value="50" label="Intronic overhang tolerance" help="The number of bp allowed to enter the intron of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 50 bp." />
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
94 <param name="no_faux_reads" type="select" label="Disable tiling of reference transcripts" help="This option disables tiling of the reference transcripts with faux reads. Use this if you only want to use sequencing reads in assembly but do not want to output assembled transcripts that lay within reference transcripts. All reference transcripts in the input annotation will also be included in the output.">
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
95 <option value="" selected="True">No</option>
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
96 <option value="--no-faux-reads">Yes</option>
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
97 </param>
2
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents: 0
diff changeset
98 </when>
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
99 </conditional>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
100 <conditional name="bias_correction">
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
101 <param name="do_bias_correction" type="select" label="Perform Bias Correction"
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
102 help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates.">
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
103 <option value="No" selected="true">No</option>
2
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents: 0
diff changeset
104 <option value="Yes">Yes</option>
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
105 </param>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
106 <when value="Yes">
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
107 <conditional name="seq_source">
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
108 <param name="index_source" type="select" label="Reference sequence data">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
109 <option value="cached" selected="true">Locally cached</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
110 <option value="history">History</option>
2
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents: 0
diff changeset
111 </param>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
112 <when value="cached">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
113 <param name="index" type="select" label="Using reference genome">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
114 <options from_data_table="fasta_indexes">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
115 <filter type="data_meta" ref="input" key="dbkey" column="1" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
116 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
117 </options>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
118 </param>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
119 </when>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
120 <when value="history">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
121 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
122 </when>
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
123 </conditional>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
124 </when>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
125 <when value="No" />
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
126 </conditional>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
127
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
128 <param name="multiread_correct" type="select" label="Use multi-read correct"
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
129 help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.">
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
130 <option value="No" selected="true">No</option>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
131 <option value="Yes">Yes</option>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
132 </param>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
133
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
134 <param name="length_correction" type="select" label="Apply length correction" help="Mode of length normalization to transcript FPKM.">
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
135 <option value="" selected="true">Cufflinks Effective Length Correction</option>
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
136 <option value="--no-effective-length-correction">Standard Length Correction</option>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
137 <option value="--no-length-correction">No Length Correction at all (use raw counts)</option>
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
138 </param>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
139
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
140 <param name="global_model" type="hidden_data" label="Global model (for use in Trackster)" optional="True"/>
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
141
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
142 <!-- advanced settings -->
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
143 <conditional name="advanced_settings">
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
144 <param name="use_advanced_settings" type="select" label="Set advanced Cufflinks options" help="">
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
145 <option value="No" selected="true">No</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
146 <option value="Yes" >Yes</option>
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
147 </param>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
148 <when value="No" />
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
149 <when value="Yes">
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
150 <param type="select" name="library_type" label="Library prep used for input reads" help="">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
151 <option value="auto" selected="True">Auto Detect</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
152 <option value="ff-firststrand">ff-firststrand</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
153 <option value="ff-secondstrand">ff-secondstrand</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
154 <option value="ff-unstranded">ff-unstranded</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
155 <option value="fr-firststrand">fr-firststrand</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
156 <option value="fr-secondstrand">fr-secondstrand</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
157 <option value="fr-unstranded" >fr-unstranded</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
158 <option value="transfrags">transfrags</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
159 </param>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
160 <param name="mask_file" type="data" format="gff3,gtf" label="Mask File" help="Ignore all alignment within transcripts in this file " optional="True" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
161 <param name="inner_mean_dist" type="integer" value="45" label="Inner mean distance" help="This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp,where each end is 50bp, you should set it as 200. The default is 45bp." />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
162 <param name="inner_dist_std_dev" type="integer" value="20" label="Inner distance standard deviation" help="The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp." />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
163 <param name="max_mle_iterations" type="integer" value="5000" label="Max MLE iterations" help="Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
164 <param name="junc_alpha" type="float" value="0.001" min="0" max="1" label="Alpha value for the binomial test used during false positive spliced alignment filtration" help="Default: 0.001" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
165 <param name="small_anchor_fraction" type="float" value="0.09" min="0" max="1" label="percent read overhang taken as suspiciously small" help="Spliced reads with less than this percent of their length on each side of the junction are considered suspicious and are candidates for filtering prior to assembly. Default: 0.09." />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
166 <param name="overhang_tolerance" type="integer" value="8" label="Intronic overhang tolerance" help="The number of bp allowed to enter the intron of a transcript when determining if a read or another transcript is mappable to/compatible with it. The default is 8 bp based on the default bowtie/TopHat parameters." />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
167 <param name="max_bundle_length" type="integer" value="3500000" label="Maximum genomic length of a given bundle" help="Default: 3,500,000bp" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
168 <param name="max_bundle_frags" type="integer" value="1000000" label="Maximum number of fragments per locus" help="Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 1,000,000" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
169 <param name="min_intron_length" type="integer" value="50" label="Minimal allowed intron size" help="Default: 50bp" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
170 <param name="trim_three_avgcov_thresh" type="integer" value="10" label="Minimum average coverage required to attempt 3prime trimming." help="Default: 10" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
171 <param name="trim_three_dropoff_frac" type="float" value="0.1" min="0" max="1" label="The fraction of average coverage below which to trim the 3prime end of an assembled transcript." help="Default: 0.1"/>
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
172 </when>
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
173 </conditional>
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
174 </inputs>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
175 <outputs>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
176 <data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.fpkm_tracking"/>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
177 <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
178 <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
179 <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
180 <data format="gtf" name="skipped" label="${tool.name} on ${on_string}: Skipped Transcripts" from_work_dir="skipped.gtf"/>
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
181 </outputs>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
182
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
183 <trackster_conf>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
184 <action name="global_model" output_name="total_map_mass"/>
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
185 </trackster_conf>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
186 <tests>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
187 <!--
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
188 Simple test that uses test data included with cufflinks.
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
189 -->
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
190 <test>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
191 <param name="input" value="cufflinks_in.bam"/>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
192 <param name="max_intron_len" value="300000"/>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
193 <param name="min_isoform_fraction" value="0.05"/>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
194 <param name="pre_mrna_fraction" value="0.05"/>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
195 <param name="use_ref" value="No"/>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
196 <param name="do_bias_correction" value="No"/>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
197 <param name="multiread_correct" value="No"/>
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
198 <param name="length_correction" value=""/>
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
199 <param name="use_advanced_settings" value="No" />
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
200 <output name="genes_expression" ftype="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
201 <output name="transcripts_expression" ftype="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/>
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
202 <output name="assembled_isoforms" file="cufflinks_out1.gtf"/>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
203 <output name="global_model" file="cufflinks_out4.txt"/>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
204 <output name="skipped" file="cufflinks_out4.gtf"/>
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
205 </test>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
206 </tests>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
207
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
208 <help>
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
209 **Cufflinks Overview**
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
210
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
211 Cufflinks_ assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. 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
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
212
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
213 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
214
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
215 ------
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
216
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
217 **Know what you are doing**
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
218
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
219 .. class:: warningmark
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
220
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
221 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.
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
222
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
223 .. __: http://cole-trapnell-lab.github.io/cufflinks/cufflinks/
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
224
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
225 ------
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
226
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
227 **Input formats**
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
228
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
229 Cufflinks takes a text file of SAM alignments as input. The RNA-Seq read mapper TopHat produces output in this format, and is recommended for use with Cufflinks. However Cufflinks will accept SAM alignments generated by any read mapper. Here's an example of an alignment Cufflinks will accept::
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
230
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
231 s6.25mer.txt-913508 16 chr1 4482736 255 14M431N11M * 0 0 \
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
232 CAAGATGCTAGGCAAGTCTTGGAAG IIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:-
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
233
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
234 Note the use of the custom tag XS. This attribute, which must have a value of "+" or "-", indicates which strand the RNA that produced this read came from. While this tag can be applied to any alignment, including unspliced ones, it must be present for all spliced alignment records (those with a 'N' operation in the CIGAR string).
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
235 The SAM file supplied to Cufflinks must be sorted by reference position. If you aligned your reads with TopHat, your alignments will be properly sorted already. If you used another tool, you may want to make sure they are properly sorted as follows::
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
236
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
237 sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
238
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
239 NOTE: Cufflinks currently only supports SAM alignments with the CIGAR match ('M') and reference skip ('N') operations. Support for the other operations, such as insertions, deletions, and clipping, will be added in the future.
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
240
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
241 ------
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
242
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
243 **Outputs**
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
244
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
245 Cufflinks produces three output files:
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
246
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
247 Transcripts and Genes:
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
248
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
249 This GTF file contains Cufflinks' assembled isoforms. The first 7 columns are standard GTF, and the last column contains attributes, some of which are also standardized (e.g. gene_id, transcript_id). There one GTF record per row, and each record represents either a transcript or an exon within a transcript. The columns are defined as follows::
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
250
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
251 Column number Column name Example Description
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
252 -----------------------------------------------------
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
253 1 seqname chrX Chromosome or contig name
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
254 2 source Cufflinks The name of the program that generated this file (always 'Cufflinks')
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
255 3 feature exon The type of record (always either "transcript" or "exon").
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
256 4 start 77696957 The leftmost coordinate of this record (where 0 is the leftmost possible coordinate)
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
257 5 end 77712009 The rightmost coordinate of this record, inclusive.
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
258 6 score 77712009 The most abundant isoform for each gene is assigned a score of 1000. Minor isoforms are scored by the ratio (minor FPKM/major FPKM)
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
259 7 strand + Cufflinks' guess for which strand the isoform came from. Always one of '+', '-' '.'
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
260 7 frame . Cufflinks does not predict where the start and stop codons (if any) are located within each transcript, so this field is not used.
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
261 8 attributes See below
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
262
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
263 Each GTF record is decorated with the following attributes::
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
264
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
265 Attribute Example Description
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
266 -----------------------------------------
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
267 gene_id CUFF.1 Cufflinks gene id
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
268 transcript_id CUFF.1.1 Cufflinks transcript id
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
269 FPKM 101.267 Isoform-level relative abundance in Reads Per Kilobase of exon model per Million mapped reads
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
270 frac 0.7647 Reserved. Please ignore, as this attribute may be deprecated in the future
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
271 conf_lo 0.07 Lower bound of the 95% confidence interval of the abundance of this isoform, as a fraction of the isoform abundance. That is, lower bound = FPKM * (1.0 - conf_lo)
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
272 conf_hi 0.1102 Upper bound of the 95% confidence interval of the abundance of this isoform, as a fraction of the isoform abundance. That is, upper bound = FPKM * (1.0 + conf_lo)
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
273 cov 100.765 Estimate for the absolute depth of read coverage across the whole transcript
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
274
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
275 Transcripts only:
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
276 This file is simply a tab delimited file containing one row per transcript and with columns containing the attributes above. There are a few additional attributes not in the table above, but these are reserved for debugging, and may change or disappear in the future.
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
277
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
278 Genes only:
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
279 This file contains gene-level coordinates and expression values.
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
280
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
281 -------
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
282
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
283 **Cufflinks settings**
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
284
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
285 All of the options have a default value. You can change any of them. Most of the options in Cufflinks have been implemented here.
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
286
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
287 ------
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
288
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
289 **Cufflinks parameter list**
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
290
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
291 This is a list of implemented Cufflinks options::
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
292
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
293 -m INT This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 45bp.
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
294 -s INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
295 -I INT The minimum intron length. Cufflinks will not report transcripts with introns longer than this, and will ignore SAM alignments with REF_SKIP CIGAR operations longer than this. The default is 300,000.
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
296 -F After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. The default is 0.05, or 5% of the most abundant isoform (the major isoform) of the gene.
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
297 -j Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%.
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 7
diff changeset
298 -G Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
299 -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.
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
300 </help>
7
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
301 <citations>
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
302 <citation type="doi">10.1038/nbt.1621</citation>
5346d5eea8b1 Uploaded
devteam
parents: 6
diff changeset
303 </citations>
0
b50aacc8ae49 Uploaded tool tarball.
devteam
parents:
diff changeset
304 </tool>