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comparison samtools_calmd.xml @ 5:ed0f72810fd5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:16:22 -0400
parents 609810451a80
children 3b6f46492fd8
comparison
equal deleted inserted replaced
4:7bf8c0f07c46 5:ed0f72810fd5
1 <tool id="samtools_calmd" name="CalMD" version="2.0"> 1 <tool id="samtools_calmd" name="CalMD" version="2.0.1">
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"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio"></expand> 7 <expand macro="stdio"/>
8 <expand macro="version_command"></expand> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 #if str( $reference_source.reference_source_selector ) == "history": 10 #if str( $reference_source.reference_source_selector ) == "history":
11 #set ref_fa = 'ref.fa' 11 #set ref_fa = 'ref.fa'
12 ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa && 12 ln -s '${reference_source.ref_fasta}' ref.fa &&
13 samtools faidx ref.fa &&
13 #else: 14 #else:
14 #set ref_fa = str( $reference_source.ref_fasta.fields.path ) 15 #set ref_fa = str( $reference_source.ref_fasta.fields.path )
15 #end if 16 #end if
17
16 samtools calmd 18 samtools calmd
17 #if str($option_set.option_sets) == 'advanced': 19 #if str($option_set.option_sets) == 'advanced':
18 $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq 20 $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq
19 #end if 21 #end if
20 -b "$input_bam" "$ref_fa" > "$calmd_output" ]]> 22 -b
21 </command> 23 '$input_bam'
24 '$ref_fa'
25 > '$calmd_output'
26 ]]></command>
22 <inputs> 27 <inputs>
23 <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" /> 28 <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" />
24 <conditional name="reference_source"> 29 <conditional name="reference_source">
25 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> 30 <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> 31 <option value="cached">Use a built-in genome</option>
27 <option value="history">Use a genome from the history</option> 32 <option value="history">Use a genome from the history</option>
28 </param> 33 </param>
29 <when value="cached"> 34 <when value="cached">
30 <param name="ref_fasta" type="select" label="Using reference genome"> 35 <param name="ref_fasta" type="select" label="Using reference genome">
31 <options from_data_table="fasta_indexes"> 36 <options from_data_table="fasta_indexes">
32 <filter type="data_meta" column="0" key="dbkey" ref="input_bam" /> 37 <filter type="data_meta" column="1" 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" /> 38 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
34 </options> 39 </options>
35 </param> 40 </param>
36 </when> 41 </when>
37 <when value="history"> 42 <when value="history">
43 <option value="default">Use defaults</option> 48 <option value="default">Use defaults</option>
44 <option value="advanced">Advanced options</option> 49 <option value="advanced">Advanced options</option>
45 </param> 50 </param>
46 <when value="default" /> 51 <when value="default" />
47 <when value="advanced"> 52 <when value="advanced">
48 <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" help="-e"/> 53 <param name="change_identical" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" />
49 <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" help="-A"/> 54 <param name="modify_quality" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" />
50 <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" help="-r"/> 55 <param name="compute_cap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" />
51 <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" help="-E"/> 56 <param name="extended_baq" argument="-E" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" />
52 </when> 57 </when>
53 </conditional> 58 </conditional>
54 </inputs> 59 </inputs>
55 <outputs> 60 <outputs>
56 <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" /> 61 <data name="calmd_output" format="bam" label="${tool.name} on ${on_string}" />
57 </outputs> 62 </outputs>
58 <tests> 63 <tests>
59 <test> 64 <test>
60 <param name="option_sets" value="default" /> 65 <param name="option_sets" value="default" />
61 <param name="input_bam" value="phiX.bam"/> 66 <param name="input_bam" value="phiX.bam"/>
62 <param name="reference_source_selector" value="history" /> 67 <param name="reference_source_selector" value="history" />
63 <param name="ref_fasta" value="phiX.fasta" /> 68 <param name="ref_fasta" value="phiX.fasta" />
64 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> 69 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
65 </test> 70 </test>
66 <test> 71 <test>
67 <param name="option_sets" value="advanced" /> 72 <param name="option_sets" value="advanced" />
68 <param name="change_identical" value="true" /> 73 <param name="change_identical" value="true" />
69 <param name="extended_baq" value="true" /> 74 <param name="extended_baq" value="true" />
70 <param name="input_bam" value="phiX.bam"/> 75 <param name="input_bam" value="phiX.bam"/>
71 <param name="reference_source_selector" value="history" /> 76 <param name="reference_source_selector" value="history" />
72 <param name="ref_fasta" value="phiX.fasta" /> 77 <param name="ref_fasta" value="phiX.fasta" />
73 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> 78 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
74 </test> 79 </test>
75 </tests> 80 </tests>
76 <help> 81 <help><![CDATA[
77 **What it does** 82 **What it does**
78 83
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:: 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.
80 85
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 ----- 86 -----
87 87
88 **NM and MD tags** 88 **NM and MD tags**
89 89
90 From SAM format specification:: 90 From the SAM format specification::
91 91
92 MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7 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 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 94
97 </help> 95 See references for more information about SAM format tags.
98 <expand macro="citations"></expand> 96 ]]></help>
97 <expand macro="citations"/>
99 </tool> 98 </tool>