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comparison maf_stats.xml @ 2:87c1c223c704 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit 1317f57940166a6326eea430443918f85b60bd95
author iuc
date Wed, 25 Oct 2023 07:38:28 +0000
parents 0c84cce7b030
children
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1:0c84cce7b030 2:87c1c223c704
1 <tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1+galaxy0"> 1 <tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.2+galaxy0">
2 <description>Alignment coverage information</description> 2 <description>Alignment coverage information</description>
3 <command> 3 <command>
4 <![CDATA[ 4 <![CDATA[
5 #if $maf_source_type.maf_source == 'cached' 5 #if $maf_source_type.maf_source == 'cached'
6 #set $tab = '\t' 6 #set $tab = '\t'
32 <options> 32 <options>
33 <filter type="data_meta" ref="input1" key="dbkey" /> 33 <filter type="data_meta" ref="input1" key="dbkey" />
34 </options> 34 </options>
35 <validator type="dataset_ok_validator" /> 35 <validator type="dataset_ok_validator" />
36 </param> 36 </param>
37 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
38 <options>
39 <filter type="data_meta" ref="input2" key="species" />
40 </options>
41 </param>
42 </when> 37 </when>
43 <when value="cached"> 38 <when value="cached">
44 <param name="mafType" type="select" label="Choose alignments"> 39 <param name="mafType" type="select" label="Choose alignments">
45 <options from_data_table="maf_indexes"> 40 <options from_data_table="maf_indexes">
46 <column name="name" index="0"/> 41 <column name="name" index="0"/>
47 <column name="value" index="1"/> 42 <column name="value" index="1"/>
48 <column name="indexed_for" index="2"/> 43 <column name="indexed_for" index="2"/>
49 <column name="exists_in_maf" index="3" /> 44 <column name="exists_in_maf" index="3" />
50 <column name="path" index="4" /> 45 <column name="path" index="4" />
51 </options>
52 </param>
53 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
54 <options from_data_table="maf_indexes">
55 <column name="value" index="3"/>
56 <filter type="multiple_splitter" column="3" separator=","/>
57 </options> 46 </options>
58 </param> 47 </param>
59 </when> 48 </when>
60 </conditional> 49 </conditional>
61 <param name="summary" type="select" label="Type of Output"> 50 <param name="summary" type="select" label="Type of Output">
85 <output name="out_file1" file="maf_stats-out2.dat"/> 74 <output name="out_file1" file="maf_stats-out2.dat"/>
86 <param name="summary" value="true"/> 75 <param name="summary" value="true"/>
87 </test> 76 </test>
88 </tests> 77 </tests>
89 <help> 78 <help>
90 **What it does** 79 **What it does**
91 80
92 This tool takes a MAF file and an interval file and relates coverage information by interval for each species. 81 This tool takes an MAF file and an interval file and relates coverage information by interval for each species.
93 If a column does not exist in the reference genome, it is not included in the output. 82 If a column does not exist in the reference genome, it is not included in the output.
94 83
95 Consider the interval: "chrX 1000 1100 myInterval" 84 Consider the interval: "chrX 1000 1100 myInterval"
96 Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this: 85 Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this:
97 86
98 chrX 1000 1100 myInterval H XXX YYY 87 chrX 1000 1100 myInterval H XXX YYY
99 88
100 chrX 1000 1100 myInterval M XXX YYY 89 chrX 1000 1100 myInterval M XXX YYY
101 90
102 chrX 1000 1100 myInterval R XXX YYY 91 chrX 1000 1100 myInterval R XXX YYY
103 92
104 93
105 where XXX and YYY are: 94 where XXX and YYY are:
106 95
107 XXX = number of nucleotides 96 XXX = number of nucleotides
108 97
109 YYY = number of gaps 98 YYY = number of gaps
110 99
111 ---- 100 ----
112 101
113 Alternatively, you can request only summary information for a set of intervals: 102 Alternatively, you can request only summary information for a set of intervals:
114 103
115 ======== =========== ======== 104 ======== =========== ========
116 #species nucleotides coverage 105 #species nucleotides coverage
117 ======== =========== ======== 106 ======== =========== ========
118 hg18 30639 0.2372 107 hg18 30639 0.2372
119 rheMac2 7524 0.0582 108 rheMac2 7524 0.0582
120 panTro2 30390 0.2353 109 panTro2 30390 0.2353
121 ======== =========== ======== 110 ======== =========== ========
122 111
123 where **coverage** is the number of nucleotides divided by the total length of the provided intervals. 112 where **coverage** is the number of nucleotides divided by the total length of the intervals provided in the BED file.
124 </help> 113 </help>
125 <citations> 114 <citations>
126 <citation type="doi">10.1093/bioinformatics/btr398</citation> 115 <citation type="doi">10.1093/bioinformatics/btr398</citation>
127 </citations> 116 </citations>
128 </tool> 117 </tool>