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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
author devteam
date Wed, 18 Jan 2017 11:44:34 -0500
parents 10dcc8027778
children
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3:10dcc8027778 4:64ed37303c15
1 <tool id="bamSplit" name="Split" version="0.0.2" force_history_refresh="True"> 1 <tool id="bamSplit" name="Split" version="2.4.0">
2 <description>BAM datasets on variety of attributes</description> 2 <description>BAM datasets on variety of attributes</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement> 4 <requirement type="package" version="2.4.0">bamtools</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 7 <![CDATA[
8 echo "BAM" > $report &amp;&amp; 8 echo "BAM" > $report &&
9 9 #for $bam_count, $input_bam in enumerate( $input_bams ):
10 #for $bam_count, $input_bam in enumerate( $input_bams ): 10 ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
11 ln -s "${input_bam}" "localbam_${bam_count}.bam" &amp;&amp; 11 ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
12 ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp; 12 #end for
13 #end for 13 bamtools
14 14 split
15 bamtools 15 #if str ( $analysis_type.analysis_type_selector ) == "-tag" :
16 split 16 ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}"
17 17 #else
18 #if str ( $analysis_type.analysis_type_selector ) == "-tag" : 18 ${analysis_type.analysis_type_selector}
19 19 #end if
20 ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}" 20 -stub split_bam
21 21 #for $bam_count, $input_bam in enumerate( $input_bams ):
22 #else 22 -in "localbam_${bam_count}.bam"
23 23 #end for
24 ${analysis_type.analysis_type_selector} 24 ]]>
25 25 </command>
26 #end if 26 <inputs>
27 27 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
28 -stub split_bam 28 <conditional name="analysis_type">
29 29 <param name="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option">
30 #for $bam_count, $input_bam in enumerate( $input_bams ): 30 <option value="-mapped">Mapping status (-mapped)</option>
31 -in "localbam_${bam_count}.bam" 31 <option value="-paired">Pairing status (-paired)</option>
32 #end for 32 <option value="-reference">Reference name (-reference)</option>
33 33 <option value="-tag">Specific tag (-tag)</option>
34 </command> 34 </param>
35 35 <when value="-mapped" />
36 <inputs> 36 <when value="-paired" />
37 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> 37 <when value="-reference" />
38 <conditional name="analysis_type"> 38 <when value="-tag">
39 <param name="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option"> 39 <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter &quot;NM&quot;"/>
40 <option value="-mapped">Mapping status (-mapped)</option> 40 </when>
41 <option value="-paired">Pairing status (-paired)</option> 41 </conditional>
42 <option value="-reference">Reference name (-reference)</option> 42 </inputs>
43 <option value="-tag">Specific tag (-tag)</option> 43 <outputs>
44 </param> 44 <data format="txt" name="report" label="BAMSplitter Run" hidden="true">
45 <when value="-mapped" /> 45 <discover_datasets pattern="split_bam\.(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true"/>
46 <when value="-paired" /> 46 </data>
47 <when value="-reference" /> 47 </outputs>
48 <when value="-tag">
49 <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter &quot;NM&quot;"/>
50 </when>
51 </conditional>
52 </inputs>
53
54 <outputs>
55 <data format="txt" name="report" label="BAMSplitter Run" hidden="true">
56 <discover_datasets pattern="split_bam\.(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true"/>
57 </data>
58 </outputs>
59 <tests> 48 <tests>
60 <test> 49 <test>
61 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> 50 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
62 <param name="analysis_type_selector" value="-mapped"/> 51 <param name="analysis_type_selector" value="-mapped"/>
63 <output name="report"> 52 <output name="report">
64 <assert_contents> 53 <assert_contents>
65 <has_line line="BAM" /> 54 <has_line line="BAM" />
66 </assert_contents> 55 </assert_contents>
67 <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/> 56 <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/>
68 </output> 57 </output>
69
70 </test> 58 </test>
71 </tests> 59 </tests>
72 <help> 60 <help>
73 **What is does** 61 **What is does**
74 62
75 BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). 63 BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
76 64
77 ----- 65 -----
111 99
112 **More information** 100 **More information**
113 101
114 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki 102 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
115 103
116 </help> 104 </help>
117 <citations> 105 <citations>
118 <citation type="doi">10.1093/bioinformatics/btr174</citation> 106 <citation type="doi">10.1093/bioinformatics/btr174</citation>
119 </citations> 107 </citations>
120 </tool> 108 </tool>