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comparison insertion_profile.xml @ 51:09846d5169fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:23:21 -0400
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50:f242ee103277 51:09846d5169fa
1 <tool id="rseqc_insertion_profile" name="Insertion Profile" version="@WRAPPER_VERSION@">
2 <description>
3 calculates the distribution of inserted nucleotides across reads
4 </description>
5
6 <macros>
7 <import>rseqc_macros.xml</import>
8 </macros>
9
10 <expand macro="requirements" />
11
12 <expand macro="stdio" />
13
14 <version_command><![CDATA[insertion_profile.py --version]]></version_command>
15
16 <command><![CDATA[
17 insertion_profile.py -i '${input}' -o output -q ${mapq} -s "${layout}"
18 ]]>
19 </command>
20
21 <inputs>
22 <expand macro="bam_param" />
23 <expand macro="mapq_param" />
24 <expand macro="layout_param" />
25 <expand macro="rscript_output_param" />
26 </inputs>
27
28 <outputs>
29 <expand macro="pdf_output_data" filename="output.insertion_profile.pdf" />
30 <expand macro="xls_output_data" filename="output.insertion_profile.xls" />
31 <expand macro="rscript_output_data" filename="output.insertion_profile.r" />
32 </outputs>
33
34 <tests>
35 <test>
36 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
37 <param name="rscript_output" value="true" />
38 <output name="outputpdf" file="output.insertion_profile.pdf" compare="sim_size" />
39 <output name="outputxls" file="output.insertion_profile.xls" />
40 <output name="outputr" file="output.insertion_profile.r" />
41 </test>
42 </tests>
43
44 <help><![CDATA[
45 insertion_profile.py
46 ++++++++++++++++++++
47
48 Calculate the distributions of inserted nucleotides across reads. Note that to
49 use this funciton, CIGAR strings within SAM/BAM file should have ‘I’ operation.
50
51 Inputs
52 ++++++
53
54 Input BAM/SAM file
55 Alignment file in BAM/SAM format.
56
57 Minimum mapping quality
58 Minimum mapping quality for an alignment to be considered as "uniquely
59 mapped". default=30
60
61 Sequencing layout
62 Denotes whether the sequecing was single-end (SE) or paired-end (PE).
63
64 Sample Output
65 ++++++++++++++
66
67 Read-1 insertion profile:
68
69 .. image:: $PATH_TO_IMAGES/out.insertion_profile.R1.png
70 :height: 600 px
71 :width: 600 px
72 :scale: 80 %
73
74 Read-2 insertion profile:
75
76 .. image:: $PATH_TO_IMAGES/out.insertion_profile.R2.png
77 :height: 600 px
78 :width: 600 px
79 :scale: 80 %
80
81 @ABOUT@
82
83 ]]>
84 </help>
85
86 <expand macro="citations" />
87
88 </tool>