Mercurial > repos > nilesh > rseqc

annotate clipping_profile.xml @ 63:27e16a30667a draft default tip

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 d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 473382134e56
children
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_clipping_profile" name="Clipping Profile" 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>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
3 estimates clipping profile of RNA-seq reads from BAM or SAM file
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 <macros>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
6 <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
7 </macros>
61
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents: 60
diff changeset
8 <expand macro="bio_tools"/>
63
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
9 <expand macro="requirements"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
10 <expand macro="stdio"/>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
11 <version_command><![CDATA[clipping_profile.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
12 <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
13 @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
14 clipping_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}"
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
15 ]]>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
16 </command>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
17 <inputs>
63
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
18 <expand macro="bam_param"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
19 <expand macro="mapq_param"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
20 <expand macro="layout_param"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
21 <expand macro="rscript_output_param"/>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
22 </inputs>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
23 <outputs>
61
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents: 60
diff changeset
24 <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" label="${tool.name} on ${on_string}: PDF"/>
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents: 60
diff changeset
25 <expand macro="xls_output_data" filename="output.clipping_profile.xls" label="${tool.name} on ${on_string}: XML"/>
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents: 60
diff changeset
26 <expand macro="rscript_output_data" filename="output.clipping_profile.r" label="${tool.name} on ${on_string}: Rscript"/>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
27 </outputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
28 <tests>
63
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
29 <test expect_num_outputs="2">
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
30 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
31 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size"/>
62
473382134e56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
iuc
parents: 61
diff changeset
32 <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
33 </test>
63
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
34 <test expect_num_outputs="3">
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
35 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
36 <param name="rscript_output" value="true"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
37 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size"/>
62
473382134e56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
iuc
parents: 61
diff changeset
38 <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/>
63
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
39 <output name="outputr" file="output.clipping_profile_r"/>
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 <help><![CDATA[
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
43 clipping_profile.py
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
44 +++++++++++++++++++
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 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
47 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
48 (This means your reads aligner should support clipped mapping).
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 Inputs
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
51 ++++++++++++++
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 Input BAM/SAM file
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
54 Alignment file in BAM/SAM format.
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
55
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
56 Minimum mapping quality
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
57 Minimum mapping quality for an alignment to be considered as "uniquely
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
58 mapped". default=30
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
59
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
60 Sequencing layout
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
61 Denotes whether the sequecing was single-end (SE) or paired-end (PE).
45
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 Sample Output
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
64 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
65
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
66 .. image:: $PATH_TO_IMAGES/clipping_good.png
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
67 :height: 600 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
68 :width: 600 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
69 :scale: 80 %
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
70
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
71 @ABOUT@
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
72
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
73 ]]>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
74 </help>
63
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents: 62
diff changeset
75 <expand macro="citations"/>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
76 </tool>