Mercurial > repos > nilesh > rseqc

annotate RPKM_saturation.xml @ 62:473382134e56 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-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:06:01 +0000
parents 5968573462fa
children 27e16a30667a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
60
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
iuc
parents: 59
diff changeset
1 <tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
2 <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
3 <macros>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
4 <import>rseqc_macros.xml</import>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
5 </macros>
61
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents: 60
diff changeset
6 <expand macro="bio_tools"/>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
7
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
8 <expand macro="requirements" />
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
9
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
10 <expand macro="stdio" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
11
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
12 <version_command><![CDATA[RPKM_saturation.py --version]]></version_command>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
13
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
14 <command><![CDATA[
60
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
iuc
parents: 59
diff changeset
15 @BAM_SAM_INPUTS@
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
iuc
parents: 59
diff changeset
16 RPKM_saturation.py -i 'input.${extension}' -o output -r '${refgene}'
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
17
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
18 #if str($strand_type.strand_specific) == "pair"
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
19 -d
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
20 #if str($strand_type.pair_type) == "sd"
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
21 '1++,1--,2+-,2-+'
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
22 #else
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
23 '1+-,1-+,2++,2--'
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
24 #end if
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
25 #end if
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
26
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
27 #if str($strand_type.strand_specific) == "single"
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
28 -d
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
29 #if str($strand_type.single_type) == "s"
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
30 '++,--'
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
31 #else
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
32 '+-,-+'
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
33 #end if
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
34 #end if
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
35
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
36 -l ${percentileFloor} -u ${percentileCeiling} -s ${percentileStep} -c ${rpkmCutoff}
59
dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
iuc
parents: 54
diff changeset
37 --mapq $mapq
dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
iuc
parents: 54
diff changeset
38 ]]></command>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
39
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
40 <inputs>
60
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
iuc
parents: 59
diff changeset
41 <expand macro="bam_sam_param" />
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
42 <expand macro="refgene_param" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
43 <expand macro="strand_type_param" />
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
44 <param name="percentileFloor" type="integer" value="5" label="Begin sampling from this percentile (default=5)" help="(--percentile-floor)"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
45 <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
46 <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
47 <param name="rpkmCutoff" type="text" value="0.01" label="Ignore transcripts with RPKM smaller than this number (default=0.01)" help="(--rpkm-cutoff)" />
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
48 <expand macro="mapq_param" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
49 <expand macro="rscript_output_param" />
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
50 </inputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
51
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
52 <outputs>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
53 <expand macro="pdf_output_data" filename="output.saturation.pdf" />
62
473382134e56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
iuc
parents: 61
diff changeset
54 <data format="tabular" name="outputxls" from_work_dir="output.eRPKM.xls" label="${tool.name} on ${on_string}: RPKM"/>
473382134e56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
iuc
parents: 61
diff changeset
55 <data format="tabular" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string}: raw count"/>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
56 <expand macro="rscript_output_data" filename="output.saturation.r" />
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
57 </outputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
58
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
59 <tests>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
60 <test>
50
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
61 <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
62 <param name="refgene" value="hg19.HouseKeepingGenes_30.bed"/>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
63 <param name="rscript_output" value="true" />
50
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
64 <output name="outputxls">
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
65 <assert_contents>
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
66 <has_n_columns n="26" />
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
67 <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" />
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
68 </assert_contents>
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
69 </output>
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
70 <output name="outputrawxls">
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
71 <assert_contents>
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
72 <has_n_columns n="26" />
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
73 <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" />
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
74 </assert_contents>
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
75 </output>
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
76 <output name="outputr">
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
77 <assert_contents>
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
78 <has_text text="pdf('output.saturation.pdf')" />
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
79 <has_line_matching expression="S5=c\(\d+\.\d+\)" />
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
80 </assert_contents>
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
lparsons
parents: 49
diff changeset
81 </output>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
82 <output name="outputpdf" file="output.saturation.pdf" compare="sim_size" />
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
83 </test>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
84 </tests>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
85
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
86 <help><![CDATA[
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
87 RPKM_saturation.py
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
88 ++++++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
89
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
90 The precision of any sample statitics (RPKM) is affected by sample size (sequencing depth);
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
91 \'resampling\' or \'jackknifing\' is a method to estimate the precision of sample statistics by
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
92 using subsets of available data. This module will resample a series of subsets from total RNA
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
93 reads and then calculate RPKM value using each subset. By doing this we are able to check if
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
94 the current sequencing depth was saturated or not (or if the RPKM values were stable or not)
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
95 in terms of genes' expression estimation. If sequencing depth was saturated, the estimated
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
96 RPKM value will be stationary or reproducible. By default, this module will calculate 20
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
97 RPKM values (using 5%, 10%, ... , 95%,100% of total reads) for each transcripts.
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
98
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
99 In the output figure, Y axis is "Percent Relative Error" or "Percent Error" which is used
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
100 to measures how the RPKM estimated from subset of reads (i.e. RPKMobs) deviates from real
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
101 expression level (i.e. RPKMreal). However, in practice one cannot know the RPKMreal. As a
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
102 proxy, we use the RPKM estimated from total reads to approximate RPKMreal.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
103
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
104 .. image:: $PATH_TO_IMAGES/RelativeError.png
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
105 :height: 80 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
106 :width: 400 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
107 :scale: 100 %
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
108
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
109 Inputs
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
110 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
111
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
112 Input BAM/SAM file
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
113 Alignment file in BAM/SAM format.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
114
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
115 Reference gene model
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
116 Gene model in BED format.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
117
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
118 Strand sequencing type (default=none)
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
119 See Infer Experiment tool if uncertain.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
120
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
121 Options
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
122 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
123
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
124 Skip Multiple Hit Reads
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
125 Use Multiple hit reads or use only uniquely mapped reads.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
126
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
127 Only use exonic reads
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
128 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
129
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
130 Output
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
131 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
132
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
133 1. output..eRPKM.xls: RPKM values for each transcript
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
134 2. output.rawCount.xls: Raw count for each transcript
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
135 3. output.saturation.r: R script to generate plot
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
136 4. output.saturation.pdf:
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
137
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
138 .. image:: $PATH_TO_IMAGES/saturation.png
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
139 :height: 600 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
140 :width: 600 px
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
141 :scale: 80 %
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
142
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
143 - All transcripts were sorted in ascending order according to expression level (RPKM). Then they are divided into 4 groups:
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
144 1. Q1 (0-25%): Transcripts with expression level ranked below 25 percentile.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
145 2. Q2 (25-50%): Transcripts with expression level ranked between 25 percentile and 50 percentile.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
146 3. Q3 (50-75%): Transcripts with expression level ranked between 50 percentile and 75 percentile.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
147 4. Q4 (75-100%): Transcripts with expression level ranked above 75 percentile.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
148 - BAM/SAM file containing more than 100 million alignments will make module very slow.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
149 - Follow example below to visualize a particular transcript (using R console)::
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
150
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
151 pdf("xxx.pdf") #starts the graphics device driver for producing PDF graphics
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
152 x &lt;- seq(5,100,5) #resampling percentage (5,10,15,...,100)
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
153 rpkm &lt;- c(32.95,35.43,35.15,36.04,36.41,37.76,38.96,38.62,37.81,38.14,37.97,38.58,38.59,38.54,38.67, 38.67,38.87,38.68, 38.42, 38.23) #Paste RPKM values calculated from each subsets
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
154 scatter.smooth(x,100*abs(rpkm-rpkm[length(rpkm)])/(rpkm[length(rpkm)]),type="p",ylab="Precent Relative Error",xlab="Resampling Percentage")
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
155 dev.off() #close graphical device
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
156
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
157 .. image:: $PATH_TO_IMAGES/saturation_eg.png
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
158 :height: 600 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
159 :width: 600 px
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
160 :scale: 80 %
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
161
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 50
diff changeset
162 @ABOUT@
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
163
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
164 ]]>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
165 </help>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
166
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
167 <expand macro="citations" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
168
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
169 </tool>