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comparison samtools_calmd.xml @ 0:39472bc02d8d draft

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Uploaded initial tool tarball.
author devteam
date Wed, 24 Sep 2014 10:43:00 -0400
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1 <tool id="samtools_calmd" name="Recalculate" version="1.0.0">
2 <description>MD/NM tags and '=' bases</description>
3 <requirements>
4 <requirement type="package" version="1.0">samtools</requirement>
5 </requirements>
6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
7 <command><![CDATA[
8 #if str( $reference_source.reference_source_selector ) == "history":
9 #set ref_fa = 'ref.fa'
10 ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa &&
11 #else:
12 #set ref_fa = str( $reference_source.ref_fasta.fields.path )
13 #end if
14 samtools calmd
15 #if str($option_set.option_sets) == 'advanced':
16 $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq
17 #end if
18 -b "$input_bam" "$ref_fa" > "$calmd_output" ]]>
19 </command>
20 <stdio>
21 <exit_code range="1:" level="fatal" description="Error" />
22 </stdio>
23 <inputs>
24 <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" />
25 <conditional name="reference_source">
26 <param name="reference_source_selector" type="select" label="Choose the source for the reference FASTA">
27 <option value="cached">Locally cached</option>
28 <option value="history">History</option>
29 </param>
30 <when value="cached">
31 <param name="ref_fasta" type="select" label="Using reference genome">
32 <options from_data_table="fasta_indexes">
33 <filter type="data_meta" column="value" key="dbkey" ref="input_bam" />
34 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
35 </options>
36 </param>
37 </when>
38 <when value="history">
39 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" />
40 </when>
41 </conditional>
42 <conditional name="option_set">
43 <param name="option_sets" type="select" label="Options">
44 <option value="default">Use defaults</option>
45 <option value="advanced">Advanced options</option>
46 </param>
47 <when value="default" />
48 <when value="advanced">
49 <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" />
50 <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" />
51 <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" />
52 <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" />
53 </when>
54 </conditional>
55 </inputs>
56 <outputs>
57 <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" />
58 </outputs>
59 <tests>
60 <test>
61 <param name="option_sets" value="default" />
62 <param name="input_bam" value="phiX.bam" dbkey="phiX" />
63 <param name="reference_source|reference_source_selector" value="history" />
64 <param name="ref_fasta" value="phiX.fasta" dbkey="phiX" />
65 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
66 </test>
67 <!-- Using the test-data-repo's phiX.fa should produce the same output. -->
68 <test>
69 <param name="option_sets" value="default" />
70 <param name="input_bam" value="phiX.bam" dbkey="phiX" />
71 <param name="reference_source|reference_source_selector" value="cached" />
72 <param name="ref_fasta" value="phiX" />
73 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
74 </test>
75 <test>
76 <param name="option_sets" value="advanced" />
77 <param name="change_identical" value="true" />
78 <param name="extended_baq" value="true" />
79 <param name="input_bam" value="phiX.bam" dbkey="phiX" />
80 <param name="reference_source|reference_source_selector" value="history" />
81 <param name="ref_fasta" value="phiX.fasta" dbkey="phiX" />
82 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
83 </test>
84 <!-- Using the test-data-repo's phiX.fa should, as before, produce the same output. -->
85 <test>
86 <param name="option_sets" value="advanced" />
87 <param name="change_identical" value="true" />
88 <param name="extended_baq" value="true" />
89 <param name="input_bam" value="phiX.bam" dbkey="phiX" />
90 <param name="reference_source|reference_source_selector" value="cached" />
91 <param name="ref_fasta" value="phiX" />
92 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
93 </test>
94 </tests>
95 <help>
96 **What it does**
97
98 Generate the MD tag. If the MD tag is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file.
99
100 ------
101
102 **Citation**
103
104 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
105
106
107 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
108
109 </help>
110 </tool>