Mercurial > repos > devteam > samtools_calmd
comparison samtools_calmd.xml @ 0:1ebb4ecdc1ef draft
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author | devteam |
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date | Tue, 21 Apr 2015 15:13:37 -0400 |
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children | 33208952b99d |
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-1:000000000000 | 0:1ebb4ecdc1ef |
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1 <tool id="samtools_calmd" name="CalMD" version="2.0"> | |
2 <description>recalculate MD/NM tags</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"></expand> | |
7 <expand macro="stdio"></expand> | |
8 <expand macro="version_command"></expand> | |
9 <command><![CDATA[ | |
10 #if str( $reference_source.reference_source_selector ) == "history": | |
11 #set ref_fa = 'ref.fa' | |
12 ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa && | |
13 #else: | |
14 #set ref_fa = str( $reference_source.ref_fasta.fields.path ) | |
15 #end if | |
16 samtools calmd | |
17 #if str($option_set.option_sets) == 'advanced': | |
18 $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq | |
19 #end if | |
20 -b "$input_bam" "$ref_fa" > "$calmd_output" ]]> | |
21 </command> | |
22 <inputs> | |
23 <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" /> | |
24 <conditional name="reference_source"> | |
25 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
26 <option value="cached">Use a built-in genome</option> | |
27 <option value="history">Use a genome from the history</option> | |
28 </param> | |
29 <when value="cached"> | |
30 <param name="ref_fasta" type="select" label="Using reference genome"> | |
31 <options from_data_table="fasta_indexes"> | |
32 <filter type="data_meta" column="0" key="dbkey" ref="input_bam" /> | |
33 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> | |
34 </options> | |
35 </param> | |
36 </when> | |
37 <when value="history"> | |
38 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" /> | |
39 </when> | |
40 </conditional> | |
41 <conditional name="option_set"> | |
42 <param name="option_sets" type="select" label="Options"> | |
43 <option value="default">Use defaults</option> | |
44 <option value="advanced">Advanced options</option> | |
45 </param> | |
46 <when value="default" /> | |
47 <when value="advanced"> | |
48 <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" help="-e"/> | |
49 <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" help="-A"/> | |
50 <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" help="-r"/> | |
51 <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" help="-E"/> | |
52 </when> | |
53 </conditional> | |
54 </inputs> | |
55 <outputs> | |
56 <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" /> | |
57 </outputs> | |
58 <tests> | |
59 <test> | |
60 <param name="option_sets" value="default" /> | |
61 <param name="input_bam" value="phiX.bam"/> | |
62 <param name="reference_source_selector" value="history" /> | |
63 <param name="ref_fasta" value="phiX.fasta" /> | |
64 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> | |
65 </test> | |
66 <test> | |
67 <param name="option_sets" value="advanced" /> | |
68 <param name="change_identical" value="true" /> | |
69 <param name="extended_baq" value="true" /> | |
70 <param name="input_bam" value="phiX.bam"/> | |
71 <param name="reference_source_selector" value="history" /> | |
72 <param name="ref_fasta" value="phiX.fasta" /> | |
73 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> | |
74 </test> | |
75 </tests> | |
76 <help> | |
77 **What it does** | |
78 | |
79 Generates the MD tag using ``samtools calmd`` command. If the MD tag (see SAM format refernce below for explanation of SAM/BAM tags) is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. The command has the following options:: | |
80 | |
81 -e change identical bases to '=' | |
82 -A modify the quality string | |
83 -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A) | |
84 -E extended BAQ for better sensitivity but lower specificity | |
85 | |
86 ----- | |
87 | |
88 **NM and MD tags** | |
89 | |
90 From SAM format specification:: | |
91 | |
92 MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7 | |
93 NM (indeger) Edit distance to the reference, including ambiguous bases but excluding clipping | |
94 | |
95 See refernces for more information about SAM format tags. | |
96 | |
97 </help> | |
98 <expand macro="citations"></expand> | |
99 </tool> |