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comparison macros.xml @ 2:6166013090c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:18:03 -0400
parents 8bfe0d1616d2
children b5c3b1856370
comparison
equal deleted inserted replaced
1:8bfe0d1616d2 2:6166013090c0
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2">samtools</requirement> 4 <requirement type="package" version="1.3.1">samtools</requirement>
5 <yield/> 5 <yield/>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8 <token name="@TOOL_VERSION@">1.3.1</token>
8 <xml name="citations"> 9 <xml name="citations">
9 <citations> 10 <citations>
10 <citation type="bibtex"> 11 <citation type="bibtex">
11 @misc{SAM_def, 12 @misc{SAM_def,
12 title={Definition of SAM/BAM format}, 13 title={Definition of SAM/BAM format},
13 url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} 14 url = {https://samtools.github.io/hts-specs/},}
14 </citation> 15 </citation>
15 <citation type="doi">10.1093/bioinformatics/btp352</citation> 16 <citation type="doi">10.1093/bioinformatics/btp352</citation>
16 <citation type="doi">10.1093/bioinformatics/btr076</citation> 17 <citation type="doi">10.1093/bioinformatics/btr076</citation>
17 <citation type="doi">10.1093/bioinformatics/btr509</citation> 18 <citation type="doi">10.1093/bioinformatics/btr509</citation>
18 <citation type="bibtex"> 19 <citation type="bibtex">
39 url = {https://github.com/samtools/samtools},} 40 url = {https://github.com/samtools/samtools},}
40 </citation> 41 </citation>
41 </citations> 42 </citations>
42 </xml> 43 </xml>
43 <xml name="version_command"> 44 <xml name="version_command">
44 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> 45 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
45 </xml> 46 </xml>
46 <xml name="stdio"> 47 <xml name="stdio">
47 <stdio> 48 <stdio>
48 <exit_code range="1:" level="fatal" description="Error" /> 49 <exit_code range="1:" level="fatal" description="Error" />
49 </stdio> 50 </stdio>
62 3. Click **Datatype** tab 63 3. Click **Datatype** tab
63 4. Set **New Type** to **BAM** 64 4. Set **New Type** to **BAM**
64 5. Click **Save** 65 5. Click **Save**
65 66
66 The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down. 67 The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
67
68 </token> 68 </token>
69
70 </macros> 69 </macros>