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comparison sam_to_bam.xml @ 0:30fdbaccb96b

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author devteam
date Mon, 26 Aug 2013 14:22:00 -0400
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1 <tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.2">
2 <description>converts SAM format to BAM format</description>
3 <requirements>
4 <requirement type="package" version="0.1.18">samtools</requirement>
5 </requirements>
6 <command interpreter="python">
7 sam_to_bam.py
8 --input1=$source.input1
9 #if $source.index_source == "history":
10 --dbkey=${ref_file.metadata.dbkey}
11 --ref_file=$source.ref_file
12 #else
13 --dbkey=${input1.metadata.dbkey}
14 #end if
15 --output1=$output1
16 --index_dir=${GALAXY_DATA_INDEX_DIR}
17 </command>
18 <inputs>
19 <conditional name="source">
20 <param name="index_source" type="select" label="Choose the source for the reference list">
21 <option value="cached">Locally cached</option>
22 <option value="history">History</option>
23 </param>
24 <when value="cached">
25 <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert">
26 <validator type="unspecified_build" />
27 <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
28 </param>
29 </when>
30 <when value="history">
31 <param name="input1" type="data" format="sam" label="Convert SAM file" />
32 <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
33 </when>
34 </conditional>
35 </inputs>
36 <outputs>
37 <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM">
38 <actions>
39 <conditional name="source.index_source">
40 <when value="cached">
41 <action type="metadata" name="dbkey">
42 <option type="from_param" name="source.input1" param_attribute="dbkey" />
43 </action>
44 </when>
45 <when value="history">
46 <action type="metadata" name="dbkey">
47 <option type="from_param" name="source.ref_file" param_attribute="dbkey" />
48 </action>
49 </when>
50 </conditional>
51 </actions>
52 </data>
53 </outputs>
54 <tests>
55 <test>
56 <!--
57 Sam-to-Bam command:
58 cp test-data/chr_m.fasta .
59 samtools faidx chr_m.fasta
60 samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
61 samtools sort unsorted.bam sam_to_bam_out1
62 chr_m.fasta is the reference file (chrM from equCab2)
63 -->
64 <param name="index_source" value="history" />
65 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" />
66 <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" />
67 <output name="output1" file="sam_to_bam_out1.bam" ftype="bam" />
68 </test>
69 <test>
70 <!--
71 Sam-to-Bam command:
72 samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
73 samtools sort unsorted.bam sam_to_bam_out2
74 chr_m.fasta is the reference file and the index chr_m.fasta.fai
75 these should be in the same directory, and chrM is from equCab2
76 -->
77 <param name="index_source" value="cached" />
78 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" />
79 <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" />
80 </test>
81 </tests>
82 <help>
83
84 **What it does**
85
86 This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file.
87
88 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
89
90 ------
91
92 **Citation**
93
94 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;`_
95
96 </help>
97 </tool>