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comparison sam_to_bam.xml @ 6:d04d9f1c6791 draft

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author devteam
date Tue, 21 Apr 2015 14:52:20 -0400
parents c73bf16b45df
children 881e16ad05c6
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5:c73bf16b45df 6:d04d9f1c6791
1 <tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.4"> 1 <tool id="sam_to_bam" name="SAM-to-BAM" version="2.0">
2 <description>converts SAM format to BAM format</description> 2 <description>convert SAM to BAM</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.1.19">samtools</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <command interpreter="python"> 6 <expand macro="requirements"></expand>
7 sam_to_bam.py 7 <expand macro="version_command"></expand>
8 --input1=$source.input1 8 <expand macro="stdio"></expand>
9 #if $source.index_source == "history": 9 <command>
10 --ref_file=$source.ref_file 10 <![CDATA[
11 #else 11 samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o sorted_input.bam -T temp "$input1" &&
12 --index=${source.index.fields.path} 12 #if $source.index_source == "history":
13 #end if 13 ln -s $source.ref_file input.fa &&
14 --output1=$output1 14 samtools faidx input.fa &&
15 </command> 15 #else
16 <inputs> 16 ln -s ${source.index.fields.path} input.fa &&
17 <conditional name="source"> 17 ln -s ${source.index.fields.path}.fai input.fa.fai &&
18 <param name="index_source" type="select" label="Choose the source for the reference list"> 18 #end if
19 <option value="cached">Locally cached</option> 19 samtools view -@ \${GALAXY_SLOTS:-1} -b -h -o $output1 -T input.fa sorted_input.bam
20 <option value="history">History</option> 20 ]]>
21 </param> 21 </command>
22 <when value="cached"> 22 <inputs>
23 <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM file to convert"> 23 <conditional name="source">
24 <validator type="unspecified_build" /> 24 <param label="Choose the source for the reference genome" name="index_source" type="select">
25 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> 25 <option value="cached">Use a built-in genome</option>
26 </param> 26 <option value="history">Use a genome from the history</option>
27 <param name="index" type="select" label="Using reference genome"> 27 </param>
28 <options from_data_table="fasta_indexes"> 28 <when value="cached">
29 <filter type="data_meta" ref="input1" key="dbkey" column="1" /> 29 <param format="sam" label="SAM file to convert" metadata_name="dbkey" name="input1" type="data">
30 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> 30 <validator type="unspecified_build" />
31 </options> 31 <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
32 </param> 32 </param>
33 </when> 33 <param label="Using reference genome" name="index" type="select">
34 <when value="history"> 34 <options from_data_table="fasta_indexes">
35 <param name="input1" type="data" format="sam" label="SAM file to convert" /> 35 <filter column="1" key="dbkey" ref="input1" type="data_meta" />
36 <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" /> 36 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
37 </when> 37 </options>
38 </conditional> 38 </param>
39 </inputs> 39 </when>
40 <outputs> 40 <when value="history">
41 <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM"> 41 <param format="sam" label="SAM file to convert" name="input1" type="data" />
42 <actions> 42 <param format="fasta" label="Using reference file" metadata_name="dbkey" name="ref_file" type="data" />
43 <conditional name="source.index_source"> 43 </when>
44 <when value="cached">
45 <action type="metadata" name="dbkey">
46 <option type="from_param" name="source.input1" param_attribute="dbkey" />
47 </action>
48 </when>
49 <when value="history">
50 <action type="metadata" name="dbkey">
51 <option type="from_param" name="source.ref_file" param_attribute="dbkey" />
52 </action>
53 </when>
54 </conditional> 44 </conditional>
55 </actions> 45 </inputs>
56 </data> 46 <outputs>
57 </outputs> 47 <data format="bam" label="${tool.name} on ${on_string}: converted BAM" name="output1">
58 <tests> 48 <actions>
59 <test> 49 <conditional name="source.index_source">
60 <!-- 50 <when value="cached">
61 Sam-to-Bam command: 51 <action name="dbkey" type="metadata">
62 cp test-data/chr_m.fasta . 52 <option name="source.input1" param_attribute="dbkey" type="from_param" />
63 samtools faidx chr_m.fasta 53 </action>
64 samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam 54 </when>
65 samtools sort unsorted.bam sam_to_bam_out1 55 <when value="history">
66 chr_m.fasta is the reference file (chrM from equCab2) 56 <action name="dbkey" type="metadata">
67 --> 57 <option name="source.ref_file" param_attribute="dbkey" type="from_param" />
68 <param name="index_source" value="history" /> 58 </action>
69 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" /> 59 </when>
70 <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" /> 60 </conditional>
71 <output name="output1" file="sam_to_bam_out1.bam" ftype="bam" /> 61 </actions>
72 </test> 62 </data>
73 <test> 63 </outputs>
74 <!-- 64 <tests>
75 Sam-to-Bam command: 65 <test>
76 samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam 66 <param name="index_source" value="history" />
77 samtools sort unsorted.bam sam_to_bam_out2 67 <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" />
78 chr_m.fasta is the reference file and the index chr_m.fasta.fai 68 <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
79 these should be in the same directory, and chrM is from equCab2 69 <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" />
80 --> 70 </test>
81 <param name="index_source" value="cached" /> 71 </tests>
82 <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" /> 72 <help>
83 <param name="index" value="chr_m" /> 73 <![CDATA[
84 <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" />
85 </test>
86 </tests>
87 <help>
88
89 **What it does** 74 **What it does**
90 75
91 This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file. 76 Converts SAM dataset into its binary, BAM, representation using ``samtools sort`` and ``view`` commands::
92 77
93 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml 78 samtools sort -O bam -o sorted_input.bam [INPUT SAM]
79 samtools view -b -h -o -T [REFERENCE GENOME] [OUTPUT BAM] sorted_input.bam
94 80
81 ]]>
95 </help> 82 </help>
96 <citations> 83 <expand macro="citations"></expand>
97 <citation type="doi">10.1093/bioinformatics/btp352</citation>
98 </citations>
99 </tool> 84 </tool>