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comparison bamtools-split.xml @ 3:10dcc8027778 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:04:47 -0500
parents fc222996ce9b
children 64ed37303c15
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2:fc222996ce9b 3:10dcc8027778
1 <tool id="bamSplit" name="Split" version="0.0.1" force_history_refresh="True"> 1 <tool id="bamSplit" name="Split" version="0.0.2" force_history_refresh="True">
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="2.3.0_2d7685d2ae">bamtools</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 7
8 echo "BAM" > $report &amp;&amp; 8 echo "BAM" > $report &amp;&amp;
9 9
10 #for $bam_count, $input_bam in enumerate( $input_bams ): 10 #for $bam_count, $input_bam in enumerate( $input_bams ):
11 ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp; 11 ln -s "${input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
12 ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp; 12 ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
13 #end for 13 #end for
14 14
15 bamtools 15 bamtools
16 split 16 split
17 17
18 #if str ( $analysis_type.analysis_type_selector ) == "-tag" : 18 #if str ( $analysis_type.analysis_type_selector ) == "-tag" :
19 19
20 ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}" 20 ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}"
21 21
22 #else 22 #else
23 23
24 ${analysis_type.analysis_type_selector} 24 ${analysis_type.analysis_type_selector}
25 25
26 #end if 26 #end if
27 27
28 -stub split_bam 28 -stub split_bam
29 29
30 #for $bam_count, $input_bam in enumerate( $input_bams ): 30 #for $bam_count, $input_bam in enumerate( $input_bams ):
31 -in "localbam_${bam_count}.bam" 31 -in "localbam_${bam_count}.bam"
32 #end for 32 #end for
33 33
34 </command> 34 </command>
35 35
36 <inputs> 36 <inputs>
37 <repeat name="input_bams" title="BAM dataset(s) to filter" min="1"> 37 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
38 <param name="input_bam" type="data" format="bam" label="BAM dataset" />
39 </repeat>
40 <conditional name="analysis_type"> 38 <conditional name="analysis_type">
41 <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="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option">
42 <option value="-mapped">Mapping status (-mapped)</option> 40 <option value="-mapped">Mapping status (-mapped)</option>
43 <option value="-paired">Pairing status (-paired)</option> 41 <option value="-paired">Pairing status (-paired)</option>
44 <option value="-reference">Reference name (-reference)</option> 42 <option value="-reference">Reference name (-reference)</option>
50 <when value="-tag"> 48 <when value="-tag">
51 <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;"/> 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;"/>
52 </when> 50 </when>
53 </conditional> 51 </conditional>
54 </inputs> 52 </inputs>
55 53
56 <outputs> 54 <outputs>
57 <data format="txt" name="report" label="BAMSplitter Run" hidden="true"> 55 <data format="txt" name="report" label="BAMSplitter Run" hidden="true">
58 <discover_datasets pattern="split_bam\.(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true"/> 56 <discover_datasets pattern="split_bam\.(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true"/>
59 </data> 57 </data>
60 </outputs> 58 </outputs>
61 <tests> 59 <tests>
62 <test> 60 <test>
63 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> 61 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
64 <param name="analysis_type_selector" value="-mapped"/> 62 <param name="analysis_type_selector" value="-mapped"/>
65 <output name="report"> 63 <output name="report">
66 <assert_contents> 64 <assert_contents>
67 <has_line line="BAM" /> 65 <has_line line="BAM" />
68 </assert_contents> 66 </assert_contents>
69 <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/> 67 <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/>
70 </output> 68 </output>
71 69
72 </test> 70 </test>
73 </tests> 71 </tests>
74 <help> 72 <help>
75 **What is does** 73 **What is does**
76 74
87 ----- 85 -----
88 86
89 **How it works** 87 **How it works**
90 88
91 The following options can be specified via "**Split BAM dataset(s) by**" dropdown:: 89 The following options can be specified via "**Split BAM dataset(s) by**" dropdown::
92 90
93 Mapping status (-mapped) split mapped/unmapped and generate two output files 91 Mapping status (-mapped) split mapped/unmapped and generate two output files
94 named (MAPPED) and (UNMAPPED) containing mapped and unmapped 92 named (MAPPED) and (UNMAPPED) containing mapped and unmapped
95 reads, respectively. 93 reads, respectively.
96 94
97 Pairing status (-paired) split single-end/paired-end alignments and generate two output files 95 Pairing status (-paired) split single-end/paired-end alignments and generate two output files
98 named (SINGLE_END) and (PAIRED_END) containing paired and unpaired 96 named (SINGLE_END) and (PAIRED_END) containing paired and unpaired
99 reads, respectively. 97 reads, respectively.
100 98
101 Reference name (-reference) split alignments by reference name. In cases of unfinished genomes with 99 Reference name (-reference) split alignments by reference name. In cases of unfinished genomes with
102 very large number of reference sequences (scaffolds) it can generate 100 very large number of reference sequences (scaffolds) it can generate
103 thousands (if not millions) of output datasets. 101 thousands (if not millions) of output datasets.
104 102
105 Specific tag (-tag) split alignments based on all values of TAG encountered. Choosing this 103 Specific tag (-tag) split alignments based on all values of TAG encountered. Choosing this
106 option from the menu will allow you to enter the tag name. As was the 104 option from the menu will allow you to enter the tag name. As was the
107 case with the reference splitting above, this option can produce very 105 case with the reference splitting above, this option can produce very
108 large number of outputs if a tag has a large number of unique values. 106 large number of outputs if a tag has a large number of unique values.
109 107