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comparison samtools_calmd.xml @ 2:e65c2cd0964c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
author iuc
date Fri, 30 Nov 2018 17:46:15 -0500
parents 33208952b99d
children 3d873744df7e
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1:33208952b99d 2:e65c2cd0964c
1 <tool id="samtools_calmd" name="CalMD" version="2.0.1"> 1 <tool id="samtools_calmd" name="CalMD" version="2.0.2">
2 <description>recalculate MD/NM tags</description> 2 <description>recalculate MD/NM tags</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
14 #else: 14 #else:
15 #set ref_fa = str( $reference_source.ref_fasta.fields.path ) 15 #set ref_fa = str( $reference_source.ref_fasta.fields.path )
16 #end if 16 #end if
17 17
18 samtools calmd 18 samtools calmd
19 $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq
19 #if str($option_set.option_sets) == 'advanced': 20 #if str($option_set.option_sets) == 'advanced':
20 $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq 21 $option_set.change_identical -C $option_set.adjust_mq
21 #end if 22 #end if
22 -b 23 -b
23 '$input_bam' 24 '$input_bam'
24 '$ref_fa' 25 '$ref_fa'
25 > '$calmd_output' 26 > '$calmd_output'
41 </when> 42 </when>
42 <when value="history"> 43 <when value="history">
43 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" /> 44 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" />
44 </when> 45 </when>
45 </conditional> 46 </conditional>
47 <conditional name="baq_settings">
48 <param name="use_baq" argument="-r" type="select"
49 label="Do you also want BAQ (Base Alignment Quality) scores to be calculated?">
50 <option value="">No</option>
51 <option value="-r">Yes, run BAQ calculation</option>
52 </param>
53 <when value="">
54 <param name="modify_quality" type="hidden" value="" />
55 <param name="extended_baq" type="hidden" value="" />
56 </when>
57 <when value="-r">
58 <param name="modify_quality" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false"
59 label="Use BAQ to cap read base qualities"
60 help="By default, BAQ scores are stored in a separate BQ tag, and the read base quality string is left untouched. When you enable this option, the BAQ scores will be used directly to modify the quality string instead." />
61 <param name="extended_baq" argument="-E" type="boolean" truevalue="-E" falsevalue="" checked="false" label="Extended BAQ for better sensitivity" />
62 </when>
63 </conditional>
46 <conditional name="option_set"> 64 <conditional name="option_set">
47 <param name="option_sets" type="select" label="Options"> 65 <param name="option_sets" type="select" label="Additional options">
48 <option value="default">Use defaults</option> 66 <option value="default">Use defaults</option>
49 <option value="advanced">Advanced options</option> 67 <option value="advanced">Advanced options</option>
50 </param> 68 </param>
51 <when value="default" /> 69 <when value="default" />
52 <when value="advanced"> 70 <when value="advanced">
53 <param name="change_identical" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" /> 71 <param name="change_identical" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False"
54 <param name="modify_quality" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" /> 72 label="Change identical bases to '='"
55 <param name="compute_cap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" /> 73 help="Replace bases in read sequences that match the reference base at that position with an equal sign" />
56 <param name="extended_baq" argument="-E" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" /> 74 <param name="adjust_mq" argument="-C" type="integer" min="0" max="255" value="0"
75 label="Coefficient to cap mapping quality of poorly mapped reads"
76 help="Higher values for this setting mean a stronger downgrade of the mapping quality of reads with excessive mismatches (50: recommended setting for reads aligned with BWA, 0: do not downgrade mapping qualities)" />
57 </when> 77 </when>
58 </conditional> 78 </conditional>
59 </inputs> 79 </inputs>
60 <outputs> 80 <outputs>
61 <data name="calmd_output" format="bam" label="${tool.name} on ${on_string}" /> 81 <data name="calmd_output" format="bam" label="${tool.name} on ${on_string}" />
62 </outputs> 82 </outputs>
63 <tests> 83 <tests>
64 <test> 84 <test>
85 <param name="use_baq" value="" />
65 <param name="option_sets" value="default" /> 86 <param name="option_sets" value="default" />
66 <param name="input_bam" value="phiX.bam"/> 87 <param name="input_bam" value="phiX.bam"/>
67 <param name="reference_source_selector" value="history" /> 88 <param name="reference_source_selector" value="history" />
68 <param name="ref_fasta" value="phiX.fasta" /> 89 <param name="ref_fasta" value="phiX.fasta" />
69 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> 90 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
70 </test> 91 </test>
71 <test> 92 <test>
93 <param name="use_baq" value="-r" />
94 <param name="extended_baq" value="true" />
72 <param name="option_sets" value="advanced" /> 95 <param name="option_sets" value="advanced" />
73 <param name="change_identical" value="true" /> 96 <param name="change_identical" value="true" />
74 <param name="extended_baq" value="true" /> 97 <param name="adjust_mq" value="50" />
75 <param name="input_bam" value="phiX.bam"/> 98 <param name="input_bam" value="phiX.bam"/>
76 <param name="reference_source_selector" value="history" /> 99 <param name="reference_source_selector" value="history" />
77 <param name="ref_fasta" value="phiX.fasta" /> 100 <param name="ref_fasta" value="phiX.fasta" />
78 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> 101 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
79 </test> 102 </test>
80 </tests> 103 </tests>
81 <help><![CDATA[ 104 <help><![CDATA[
82 **What it does** 105 **What it does**
83 106
84 Generates the MD tag using the ``samtools calmd`` command. If the MD tag (see SAM format reference 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. 107 Generates the MD tag using the ``samtools calmd`` command. If the MD tag (see
108 SAM format reference below for explanation of SAM/BAM tags) is already present,
109 this command will give a warning if the MD tag generated is different from the
110 existing tag.
111
112 Optionally, also generates the BQ tag to encode base alignment qualities,
113 caps the mapping quality of poorly mapping reads, and modifies read sequences
114 replacing bases matching the reference with ``=``.
115
116 Outputs a BAM file.
85 117
86 ----- 118 -----
87 119
88 **NM and MD tags** 120 **SAM/BAM tags written by this tool**
89 121
90 From the SAM format specification:: 122 From the SAM format tag specification::
91 123
92 MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7 124 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 125 NM (integer) Edit distance to the reference, including ambiguous bases but excluding clipping
126 BQ (string) String of offsets to base alignment quality (BAQ), of the same length as the read sequence.
127 At the i-th read base, BAQ i = Q i − (BQ i − 64) where Q i is the i-th base quality.
94 128
95 See references for more information about SAM format tags. 129 See references for more information about SAM format tags.
96 ]]></help> 130 ]]></help>
97 <expand macro="citations"/> 131 <expand macro="citations"/>
98 </tool> 132 </tool>