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comparison samtools_calmd.xml @ 9:76f30c6db118 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 15:59:24 +0000
parents d29b421f5aaf
children dae754b6a98b
comparison
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8:d29b421f5aaf 9:76f30c6db118
1 <tool id="samtools_calmd" name="CalMD" version="2.0.2"> 1 <tool id="samtools_calmd" name="Samtools calmd" version="2.0.3" profile="@PROFILE@">
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"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @ADDTHREADS@ 10 @ADDTHREADS@
11 #if str( $reference_source.reference_source_selector ) == "history": 11 @PREPARE_FASTA_IDX@
12 #set ref_fa = 'ref.fa'
13 ln -s '${reference_source.ref_fasta}' ref.fa &&
14 samtools faidx ref.fa &&
15 #else:
16 #set ref_fa = str( $reference_source.ref_fasta.fields.path )
17 #end if
18 12
19 samtools calmd 13 samtools calmd
20 $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq 14 $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq
21 #if str($option_set.option_sets) == 'advanced': 15 #if str($option_set.option_sets) == 'advanced':
22 $option_set.change_identical -C $option_set.adjust_mq 16 $option_set.change_identical -C $option_set.adjust_mq
23 #end if 17 #end if
24 -b 18 -b
25 -@ \$addthreads 19 -@ \$addthreads
26 '$input_bam' 20 '$input'
27 '$ref_fa' 21 '$reffa'
28 > '$calmd_output' 22 > '$calmd_output'
29 ]]></command> 23 ]]></command>
30 <inputs> 24 <inputs>
31 <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" /> 25 <param name="input" type="data" format="bam" label="BAM file to recalculate" />
32 <conditional name="reference_source"> 26 <expand macro="mandatory_reference"/>
33 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
34 <option value="cached">Use a built-in genome</option>
35 <option value="history">Use a genome from the history</option>
36 </param>
37 <when value="cached">
38 <param name="ref_fasta" type="select" label="Using reference genome">
39 <options from_data_table="fasta_indexes">
40 <filter type="data_meta" column="dbkey" key="dbkey" ref="input_bam" />
41 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
42 </options>
43 </param>
44 </when>
45 <when value="history">
46 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" />
47 </when>
48 </conditional>
49 <conditional name="baq_settings"> 27 <conditional name="baq_settings">
50 <param name="use_baq" argument="-r" type="select" 28 <param name="use_baq" argument="-r" type="select"
51 label="Do you also want BAQ (Base Alignment Quality) scores to be calculated?"> 29 label="Do you also want BAQ (Base Alignment Quality) scores to be calculated?">
52 <option value="">No</option> 30 <option value="">No</option>
53 <option value="-r">Yes, run BAQ calculation</option> 31 <option value="-r">Yes, run BAQ calculation</option>
84 </outputs> 62 </outputs>
85 <tests> 63 <tests>
86 <test> 64 <test>
87 <param name="use_baq" value="" /> 65 <param name="use_baq" value="" />
88 <param name="option_sets" value="default" /> 66 <param name="option_sets" value="default" />
89 <param name="input_bam" value="phiX.bam"/> 67 <param name="input" value="phiX.bam"/>
90 <param name="reference_source_selector" value="history" /> 68 <param name="addref_select" value="history" />
91 <param name="ref_fasta" value="phiX.fasta" /> 69 <param name="ref" value="phiX.fasta" />
92 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> 70 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" lines_diff="4" />
93 </test> 71 </test>
94 <test> 72 <test>
95 <param name="use_baq" value="-r" /> 73 <param name="use_baq" value="-r" />
96 <param name="extended_baq" value="true" /> 74 <param name="extended_baq" value="true" />
97 <param name="option_sets" value="advanced" /> 75 <param name="option_sets" value="advanced" />
98 <param name="change_identical" value="true" /> 76 <param name="change_identical" value="true" />
99 <param name="adjust_mq" value="50" /> 77 <param name="adjust_mq" value="50" />
100 <param name="input_bam" value="phiX.bam"/> 78 <param name="input" value="phiX.bam"/>
101 <param name="reference_source_selector" value="history" /> 79 <param name="addref_select" value="history" />
102 <param name="ref_fasta" value="phiX.fasta" /> 80 <param name="ref" value="phiX.fasta" />
103 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> 81 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" lines_diff="4" />
104 </test> 82 </test>
105 </tests> 83 </tests>
106 <help><![CDATA[ 84 <help><![CDATA[
107 **What it does** 85 **What it does**
108 86
123 101
124 From the SAM format tag specification:: 102 From the SAM format tag specification::
125 103
126 MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7 104 MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7
127 NM (integer) Edit distance to the reference, including ambiguous bases but excluding clipping 105 NM (integer) Edit distance to the reference, including ambiguous bases but excluding clipping
128 BQ (string) String of offsets to base alignment quality (BAQ), of the same length as the read sequence. 106 BQ (string) String of offsets to base alignment quality (BAQ), of the same length as the read sequence.
129 At the i-th read base, BAQ i = Q i − (BQ i − 64) where Q i is the i-th base quality. 107 At the i-th read base, BAQ i = Q i − (BQ i − 64) where Q i is the i-th base quality.
130 108
131 See references for more information about SAM format tags. 109 See references for more information about SAM format tags.
132 ]]></help> 110 ]]></help>
133 <expand macro="citations"/> 111 <expand macro="citations"/>