Mercurial > repos > devteam > samtools_split
annotate samtools_split.xml @ 1:b7f7826ef1cd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author | iuc |
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date | Tue, 09 May 2017 11:18:30 -0400 |
parents | 57f3e32f809d |
children | 135c85f4cfaf |
rev | line source |
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b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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1 <tool id="samtools_split" name="Split" version="@TOOL_VERSION@"> |
0 | 2 <description>BAM dataset on readgroups</description> |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
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b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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6 <expand macro="requirements"/> |
b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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7 <expand macro="stdio"/> |
b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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8 <expand macro="version_command"/> |
0 | 9 <command><![CDATA[ |
10 samtools split -f 'Read_Group_%!.bam' | |
11 #if $header: | |
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b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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12 -u '${output}:${header}' |
0 | 13 #else: |
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b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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0
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changeset
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14 -u '${output}' |
0 | 15 #end if |
16 "${input_bam}" | |
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b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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changeset
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17 ]]></command> |
0 | 18 <inputs> |
19 <param name="input_bam" type="data" format="bam" label="BAM file" /> | |
1
b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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20 <param name="header" type="data" format="bam,sam" optional="True" label="Replace header in output file" /> |
0 | 21 </inputs> |
22 <outputs> | |
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b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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0
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changeset
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23 <data name="output" format="bam" label="${tool.name} on ${on_string}"> |
0 | 24 <discover_datasets pattern="Read_Group_(?P<designation>.+)\.bam" ext="bam" visible="true" directory="" /> |
25 </data> | |
26 </outputs> | |
27 <tests> | |
28 <test> | |
29 <param name="input_bam" value="phiX.bam" ftype="bam" /> | |
30 <output name="output" file="samtools_split_out.bam"> | |
31 <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" /> | |
32 <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" /> | |
33 <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" /> | |
34 </output> | |
35 </test> | |
36 </tests> | |
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b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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37 <help><![CDATA[ |
0 | 38 **What it does** |
39 | |
40 Splits BAM files on readgroups. | |
41 | |
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b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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42 This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset. |
b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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43 ]]></help> |
b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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changeset
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44 <expand macro="citations"/> |
0 | 45 </tool> |