Mercurial > repos > nilesh > rseqc

annotate geneBody_coverage2.xml @ 58:1a052c827e88 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 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 15:56:37 -0500
parents daae0a118c36
children dbedfc5f5a3c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
56
daae0a118c36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 62d3a29f93f3f6cb3ba9683fde5ff0606b90700d
iuc
parents: 54
diff changeset
1 <tool id="rseqc_geneBody_coverage2" name="Gene Body Coverage (Bigwig)" version="@WRAPPER_VERSION@.1">
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
2 <description>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
3 Read coverage over gene body
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
4 </description>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
5
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
6 <macros>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
7 <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
8 </macros>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
9
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
10 <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
11
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
12 <expand macro="stdio" />
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 <version_command><![CDATA[geneBody_coverage2.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
15
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
16 <command><![CDATA[
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
17 geneBody_coverage2.py -i '${input}' -r '${refgene}' -o output
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
18 ]]>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
19 </command>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
20
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
21 <inputs>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
22 <param name="input" type="data" label="Input bigwig file" format="bigwig" />
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
23 <expand macro="refgene_param" />
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
24 </inputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
25
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
26 <outputs>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
27 <expand macro="pdf_output_data" filename="output.geneBodyCoverage.pdf" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
28 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
29 <expand macro="rscript_output_data" filename="output.geneBodyCoverage_plot.r" />
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
30 </outputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
31
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
32 <tests>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
33 <test>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
34 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
35 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
36 <param name="rscript_output" value="true" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
37 <output name="outputpdf" file="output.geneBodyCoverage2.curves.pdf" compare="sim_size" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
38 <output name="outputr" file="output.geneBodyCoverage2.r" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
39 <output name="outputtxt" file="output.geneBodyCoverage2.txt" />
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
40 </test>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
41 </tests>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
42
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
43 <help><![CDATA[
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
44 geneBody_coverage2.py
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
45 +++++++++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
46
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
47 Similar to geneBody_coverage.py. This module takes bigwig instead of BAM as input, and thus
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
48 requires much less memory. The BigWig file could be arbitrarily large.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
49
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
50
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
51 Inputs
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
52 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
53
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
54 Input BAM/SAM file
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
55 Alignment file in BAM/SAM format.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
56
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
57 Reference gene model
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
58 Gene Model in BED format.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
59
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
60
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
61 Outputs
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
62 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
63
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
64 Read coverage over gene body. This module is used to check if reads coverage is uniform and if there is any 5’/3’ bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates a plot illustrating the coverage profile along the gene body. NOTE: this module requires lots of memory for large BAM files, because it load the entire BAM file into memory. We add another script "geneBody_coverage2.py" into v2.3.1 which takes bigwig (instead of BAM) as input. It only use 200M RAM, but users need to convert BAM into WIG, and then WIG into BigWig.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
65
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
66 Example output:
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
67 .. image:: $PATH_TO_IMAGES/geneBody_coverage.png
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
68 :height: 600 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
69 :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
70 :scale: 80 %
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
71
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
72 @ABOUT@
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
73
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
74 ]]>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
75 </help>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
76
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
77 <expand macro="citations" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
78
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
79 </tool>