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

リビジョン 2, 1.1 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.0">
2  <requirements>
3    <requirement type="package">samtools</requirement>
4  </requirements>
5  <description>converts BAM format to SAM format</description>
6  <command interpreter="python">bam_to_sam.py --input1=$input1 --output1=$output1</command>
7  <inputs>
8    <param name="input1" type="data" format="bam" label="BAM File to Convert" />
9  </inputs>
10  <outputs>
11    <data name="output1" format="sam" />
12  </outputs>
13  <tests>
14    <test>
15      <!--
16      Bam-to-Sam command:
17      samtools view -o test-data/3.bam bam_to_sam_out1.sam
18      -->
19      <param name="input1" value="1.bam" ftype="bam" />
20      <output name="output1" file="bam_to_sam_out1.sam" />
21    </test>
22    <test>
23      <!--
24      Bam-to-Sam command:
25      samtools view -o test-data/1.sam bam_to_sam_out2.sam
26      -->
27      <param name="input1" value="3.bam" ftype="bam" />
28      <param name="output1" file="bam_to_sam_out2.sam" />
29    </test>
30  </tests>
31  <help>
32
33**What it does**
34
35This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file.
36
37.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
38
39  </help>
40</tool>
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