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comparison deletion_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_deletion_profile" name="Deletion Profile" version="@WRAPPER_VERSION@">
2 <description>
3 calculates the distributions of deleted 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[deletion_profile.py --version]]></version_command>
15
16 <command><![CDATA[
17 deletion_profile.py -i '${input}' -o output -l ${readlength} -n ${readnum} -q ${mapq}
18 ]]>
19 </command>
20
21 <inputs>
22 <expand macro="bam_param" />
23 <expand macro="readlength_param" />
24 <expand macro="readnum_param" />
25 <expand macro="mapq_param" />
26 <expand macro="rscript_output_param" />
27 </inputs>
28
29 <outputs>
30 <expand macro="pdf_output_data" filename="output.deletion_profile.pdf" />
31 <expand macro="xls_output_data" filename="output.deletion_profile.txt" />
32 <expand macro="rscript_output_data" filename="output.deletion_profile.r" />
33 </outputs>
34
35 <tests>
36 <test>
37 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
38 <param name="readlength" value="101" />
39 <param name="rscript_output" value="true" />
40 <output name="outputpdf" file="output.deletion_profile.pdf" compare="sim_size" />
41 <output name="outputxls" file="output.deletion_profile.txt" />
42 <output name="outputr" file="output.deletion_profile.r" />
43 </test>
44 </tests>
45
46 <help><![CDATA[
47 deletion_profile.py
48 +++++++++++++++++++
49
50 Calculate the distributions of deleted nucleotides across reads.
51
52 Inputs
53 ++++++
54
55 Input BAM/SAM file
56 Alignment file in BAM/SAM format.
57
58 Alignment length of read
59 It is usually set to the orignial read length. For example, all these cigar
60 strings ("101M", "68M140N33M", "53M1D48M") suggest the read alignment
61 length is 101. [required]
62
63 Number of aligned reads used
64 Number of aligned reads with deletions used to calculate the deletion
65 profile. default=1000000
66
67 Minimum mapping quality
68 Minimum mapping quality for an alignment to be considered as "uniquely
69 mapped". default=30
70
71 Sample Output
72 ++++++++++++++
73
74 .. image:: $PATH_TO_IMAGES/out.deletion_profile.png
75 :height: 600 px
76 :width: 600 px
77 :scale: 80 %
78
79 @ABOUT@
80
81 ]]>
82
83 </help>
84
85 <expand macro="citations" />
86
87 </tool>