Mercurial > repos > nilesh > rseqc
annotate deletion_profile.xml @ 63:27e16a30667a draft default tip
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 |
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_deletion_profile" name="Deletion Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
2 <description> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
3 calculates the distributions of deleted nucleotides across reads |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
4 </description> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
5 <macros> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
6 <import>rseqc_macros.xml</import> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
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"/> |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
11 <version_command><![CDATA[deletion_profile.py --version]]></version_command> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
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 deletion_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq} |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
15 ]]> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
16 </command> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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="readlength_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="readnum_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="mapq_param"/> |
27e16a30667a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents:
62
diff
changeset
|
22 <expand macro="rscript_output_param"/> |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
23 </inputs> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
24 <outputs> |
63
27e16a30667a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents:
62
diff
changeset
|
25 <expand macro="pdf_output_data" filename="output.deletion_profile.pdf"/> |
27e16a30667a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents:
62
diff
changeset
|
26 <expand macro="xls_output_data" filename="output.deletion_profile.txt"/> |
27e16a30667a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents:
62
diff
changeset
|
27 <expand macro="rscript_output_data" filename="output.deletion_profile.r"/> |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
28 </outputs> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
29 <tests> |
63
27e16a30667a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents:
62
diff
changeset
|
30 <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
|
31 <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
|
32 <param name="read_align_length" value="101"/> |
27e16a30667a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents:
62
diff
changeset
|
33 <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
|
34 <output name="outputpdf" file="output.deletion_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
|
35 <output name="outputxls" file="output.deletion_profile.txt" 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
|
36 <output name="outputr" file="output.deletion_profile_r"/> |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
37 </test> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
38 </tests> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
39 <help><![CDATA[ |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
40 deletion_profile.py |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
41 +++++++++++++++++++ |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
42 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
43 Calculate the distributions of deleted nucleotides across reads. |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
44 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
45 Inputs |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
46 ++++++ |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
47 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
48 Input BAM/SAM file |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
49 Alignment file in BAM/SAM format. |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
50 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
51 Alignment length of read |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
52 It is usually set to the orignial read length. For example, all these cigar |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
53 strings ("101M", "68M140N33M", "53M1D48M") suggest the read alignment |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
54 length is 101. [required] |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
55 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
56 Number of aligned reads used |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
57 Number of aligned reads with deletions used to calculate the deletion |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
58 profile. default=1000000 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
59 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
60 Minimum mapping quality |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
61 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:
diff
changeset
|
62 mapped". default=30 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
63 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
64 Sample Output |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
65 ++++++++++++++ |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
66 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
67 .. image:: $PATH_TO_IMAGES/out.deletion_profile.png |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
68 :height: 600 px |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
69 :width: 600 px |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
70 :scale: 80 % |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
71 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
72 @ABOUT@ |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
73 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
74 ]]> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
75 |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
76 </help> |
63
27e16a30667a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
iuc
parents:
62
diff
changeset
|
77 <expand macro="citations"/> |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
diff
changeset
|
78 </tool> |