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comparison samtools_calmd.xml @ 0:1ebb4ecdc1ef draft

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author devteam
date Tue, 21 Apr 2015 15:13:37 -0400
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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>