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comparison bam_to_sam.xml @ 5:f57df915aa10 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:18:39 -0400
parents af7c50162f0b
children 10184eaa85fc
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4:af7c50162f0b 5:f57df915aa10
1 <tool id="bam_to_sam" name="BAM-to-SAM" version="2.0"> 1 <tool id="bam_to_sam" name="BAM-to-SAM" version="2.0.1">
2 <macros> 2 <description>convert BAM to SAM</description>
3 <import>macros.xml</import> 3
4 </macros> 4 <macros>
5 <expand macro="requirements"></expand> 5 <import>macros.xml</import>
6 <expand macro="version_command"></expand> 6 </macros>
7 <expand macro="stdio"></expand> 7 <expand macro="requirements"/>
8 <description>convert BAM to SAM</description> 8 <expand macro="stdio"/>
9 <command> 9 <expand macro="version_command"/>
10 <![CDATA[ 10
11 samtools view -o "${output1}" ${header} "${input1}" 11 <command><![CDATA[
12 ]]> 12 samtools view -o '${output1}' ${header} '${input1}'
13 </command> 13 ]]></command>
14
14 <inputs> 15 <inputs>
15 <param format="bam" label="BAM File to Convert" name="input1" type="data" /> 16 <param format="bam" name="input1" type="data" label="BAM File to Convert" />
16 <param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only."> 17 <param name="header" label="Header options" type="select"
18 help="Allows to choose between seeing the entire dataset with the header, header only, or data only.">
17 <option value="-h">Include header in SAM output (-h)</option> 19 <option value="-h">Include header in SAM output (-h)</option>
18 <option value="-H">Print header only (-H)</option> 20 <option value="-H">Return header only (-H)</option>
19 <option value="">Exclude header</option> 21 <option value="">Exclude header</option>
20 </param> 22 </param>
21 </inputs> 23 </inputs>
22 <outputs> 24 <outputs>
23 <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" /> 25 <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
24 </outputs> 26 </outputs>
25 <tests> 27 <tests>
26 <test> 28 <test>
27 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> 29 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
28 <param name="header" value="-h" /> 30 <param name="header" value="-h" />
29 <output file="bam_to_sam_out1.sam" name="output1" sorted="True" /> 31 <output file="bam_to_sam_out1.sam" name="output1" />
30 </test> 32 </test>
31 <test> 33 <test>
32 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> 34 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
33 <param name="header" value="-H" /> 35 <param name="header" value="-H" />
34 <output file="bam_to_sam_out2.sam" name="output1" sorted="True" /> 36 <output file="bam_to_sam_out2.sam" name="output1" />
35 </test> 37 </test>
36 <test> 38 <test>
37 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> 39 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
38 <param name="header" value="" /> 40 <param name="header" value="" />
39 <output file="bam_to_sam_out3.sam" name="output1" sorted="True" /> 41 <output file="bam_to_sam_out3.sam" name="output1" />
40 </test> 42 </test>
41 </tests> 43 </tests>
42 <help> 44 <help><![CDATA[
43 <![CDATA[
44
45 **What it does** 45 **What it does**
46 46
47 Converts BAM dataset to SAM using ``samtools view`` command:: 47 Converts BAM dataset to SAM using the ``samtools view`` command.
48 48 ]]></help>
49 samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM] 49 <expand macro="citations"/>
50
51 ]]>
52 </help>
53 <expand macro="citations"></expand>
54 </tool> 50 </tool>