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

リビジョン 2, 2.7 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="sam_merge" name="Merge BAM Files" version="1.1.0">
2  <description>merges BAM files together</description>
3  <requirements>
4    <requirement type="package">samtools</requirement>
5  </requirements>
6  <command interpreter="python">
7   sam_merge.py
8      $input1
9      $output1
10      $input2
11      #for $i in $inputs
12        ${i.input}
13      #end for
14  </command>
15  <inputs>
16    <param name="input1" label="First file" type="data" format="bam" />
17    <param name="input2" label="with file" type="data" format="bam" help="Need to add more files? Use controls below." />
18    <repeat name="inputs" title="Input Files">
19      <param name="input" label="Add file" type="data" format="bam" />
20    </repeat>
21  </inputs>
22  <outputs>
23    <data name="output1" format="bam" />
24  </outputs>
25  <tests>
26    <!-- TODO: add ability to test framework to test without at least
27         one repeat element value
28    <test>
29    -->
30      <!--
31      Bam merge command:
32      samtools merge test-data/sam_merge_out1.bam test-data/sam_merge_in1.bam test-data/sam_merge_in2.bam
33      -->
34    <!--
35      <param name="input1" value="sam_merge_in1.bam" ftype="bam" />
36      <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
37      <output name="output1" file="sam_merge_out1.bam" ftype="bam" />
38    </test>
39    -->
40    <test>
41      <!--
42      Bam merge command:
43      samtools merge test-data/sam_merge_out2.bam test-data/sam_merge_in1.bam test-data/sam_merge_in2.bam test-data/sam_merge_in3.bam
44      -->
45      <param name="input1" value="sam_merge_in1.bam" ftype="bam" />
46      <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
47      <param name="input" value="sam_merge_in3.bam" ftype="bam" />
48      <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
49    </test>
50    <!-- TODO: add ability to test code to be able to test with multiple
51         inputs (parameters with same value)
52    <test>
53    -->
54      <!--
55      Bam merge command:
56      samtools merge test-data/sam_merge_out3.bam test-data/sam_merge_in1.bam test-data/sam_merge_in2.bam test-data/sam_merge_in3.bam test-data/sam_merge_in4.bam
57      -->
58    <!--
59      <param name="input1" value="sam_merge_in1.bam" ftype="bam" />
60      <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
61      <param name="input" value="sam_merge_in3.bam" ftype="bam" />
62      <param name="input" value="sam_merge_in4.bam" ftype="bam" />
63      <output name="output1" file="sam_merge_out3.bam" ftype="bam" />
64    </test>
65    -->
66  </tests>
67  <help>
68
69**What it does**
70
71This tool uses SAMTools_' merge command to merge any number of BAM files together into one BAM file.
72
73.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
74
75  </help>
76</tool>
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