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comparison mismatch_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_mismatch_profile" name="Mismatch Profile" version="@WRAPPER_VERSION@">
2 <description>
3 calculates the distribution of mismatches 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[mismatch_profile.py --version]]></version_command>
15
16 <command><![CDATA[
17 mismatch_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.mismatch_profile.pdf" />
31 <expand macro="xls_output_data" filename="output.mismatch_profile.xls" />
32 <expand macro="rscript_output_data" filename="output.mismatch_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.mismatch_profile.pdf" compare="sim_size" />
41 <output name="outputxls" file="output.mismatch_profile.xls"/>
42 <output name="outputr" file="output.mismatch_profile.r"/>
43 </test>
44 </tests>
45
46 <help><![CDATA[
47 mismatch_profile.py
48 +++++++++++++++++++
49
50 Calculate the distribution of mismatches across reads.
51
52 Note that the “MD” tag must exist in BAM file.
53
54 Inputs
55 ++++++
56
57 Input BAM/SAM file
58 Alignment file in BAM/SAM format.
59
60 Alignment length of read
61 It is usually set to the orignial read length. For example, all these cigar
62 strings ("101M", "68M140N33M", "53M1D48M") suggest the read alignment
63 length is 101. [required]
64
65 Number of aligned reads used
66 Number of aligned reads with deletions used to calculate the deletion
67 profile. default=1000000
68
69 Minimum mapping quality
70 Minimum mapping quality for an alignment to be considered as "uniquely
71 mapped". default=30
72
73 Sample Output
74 ++++++++++++++
75
76 .. image:: $PATH_TO_IMAGES/mismatch_profile.png
77 :height: 600 px
78 :width: 600 px
79 :scale: 80 %
80
81 @ABOUT@
82
83 ]]>
84
85 </help>
86
87 <expand macro="citations" />
88
89 </tool>