root/galaxy-central/tools/samtools/sam_to_bam.xml

リビジョン 2, 2.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.0">
2  <description>converts SAM format to BAM format</description>
3  <requirements>
4    <requirement type="package">samtools</requirement>
5  </requirements>
6  <command interpreter="python">
7sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey}
8#if $source.index_source == "history":
9--ref_file=$source.ref_file
10#else
11--ref_file="None"
12#end if
13--output1=$output1 --index_dir=${GALAXY_DATA_INDEX_DIR}
14  </command>
15  <inputs>
16    <conditional name="source">
17      <param name="index_source" type="select" label="Choose the source for the reference list">
18        <option value="cached">Locally cached</option>
19        <option value="history">History</option>
20      </param>
21      <when value="cached">
22        <param name="input1" type="data" format="sam" label="SAM File to Convert">
23           <validator type="unspecified_build" />
24           <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" />
25        </param>
26      </when>
27      <when value="history">
28        <param name="input1" type="data" format="sam" label="Convert SAM file" />
29        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
30      </when>
31    </conditional>
32  </inputs>
33  <outputs>
34    <data name="output1" format="bam"/>
35  </outputs>
36  <tests>
37    <test>
38      <!--
39      Sam-to-Bam command:
40      samtools faidx chr_m.fasta
41      samtools view -bt chr_m.fasta.fai -o unsorted.bam test-data/3.sam
42      samtools sort unsorted.bam sam_to_bam_out1
43      chr_m.fasta is the reference file
44      -->
45      <param name="index_source" value="history" />
46      <param name="input1" value="3.sam" ftype="sam" />
47      <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" />
48      <output name="output1" file="sam_to_bam_out1.bam" />
49    </test>
50    <test>
51      <!--
52      Sam-to-Bam command:
53      samtools view -bt chr_m.fasta.fai -o unsorted.bam test-data/3.sam
54      samtools sort unsorted.bam sam_to_bam_out2
55      chr_m.fasta is the reference file and the index chr_m.fasta.fai
56      should be in the same directory
57      -->
58      <param name="index_source" value="cached" />
59      <param name="input1" value="3.sam" ftype="sam" dbkey="equCab2" />
60      <param name="output1" file="sam_to_bam_out2.bam" />
61    </test>
62  </tests>
63  <help>
64
65**What it does**
66
67This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file.
68
69.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
70
71  </help>
72</tool>
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