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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
author artbio
date Thu, 20 Jul 2023 00:28:10 +0000
parents b3107800eea7
children
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0:b3107800eea7 1:075419d27ca3
1 <tool id="bamparse" name="Count alignments" version="4.0.0"> 1 <tool id="bamparse" name="Count alignments" version="4.1.0">
2 <description>in a BAM file</description> 2 <description>in a BAM file</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.21.0=py310h41dec4a_1">pysam</requirement> 4 <requirement type="package" version="0.21.0=py310h41dec4a_1">pysam</requirement>
5 <requirement type="package" version="1.0=h98b6b92_0">sambamba</requirement> 5 <requirement type="package" version="1.0=h98b6b92_0">sambamba</requirement>
6 <requirement type="package" version="1.17=hd87286a_1">samtools</requirement> 6 <requirement type="package" version="1.17=hd87286a_1">samtools</requirement>
28 #end for 28 #end for
29 --labels 29 --labels
30 #for $file in $input_list 30 #for $file in $input_list
31 '$file.element_identifier' 31 '$file.element_identifier'
32 #end for 32 #end for
33 --number '$output_option' 33 --number '$output_option' &&
34 #if $output_option == 'unique':
35 cp ./outputdir/table.tabular $table
36 #else if $output_option == 'multiple':
37 cp outputdir/* ./ && ls -latr ./
38 #end if
34 ]]></command> 39 ]]></command>
35 <inputs> 40 <inputs>
36 <param name="input_list" type="data" format="bam" label="Select multiple alignments to parse" multiple="true"/> 41 <param name="input_list" type="data" format="bam" label="Select multiple alignments to parse" multiple="true"/>
37 <param name="polarity" type="select" label="how to count sense and antisense reads"> 42 <param name="polarity" type="select" label="how to count sense and antisense reads">
38 <option value="both">count both sense and antisense reads</option> 43 <option value="both">count both sense and antisense reads</option>
39 <option value="sense">count only sense reads</option> 44 <option value="sense">count only sense reads</option>
40 <option value="antisense">count only antisense reads</option> 45 <option value="antisense">count only antisense reads</option>
41 </param> 46 </param>
42 <param name="output_option" type="select" display="radio" label="Select the number of files for results" 47 <param name="output_option" type="select" display="radio" label="Select the number of files for results"
43 help="Results can be returned either as a single multi-column table or in separate two-column 48 help="Results can be returned either as a single multi-column table or in a collection of separate two-column
44 datasets (useful for DESeq subsequent analysis)"> 49 datasets (useful for DESeq subsequent analysis)">
45 <option value="unique">A multi-column table</option> 50 <option value="unique">A multi-column table</option>
46 <option value="multiple">One separate two-columns dataset per input bam alignment</option> 51 <option value="multiple">One separate two-columns dataset per input bam alignment</option>
47 </param> 52 </param>
48 </inputs> 53 </inputs>
49 <outputs> 54 <outputs>
50 <data name="output" format="tabular" label="Counts"> 55 <data name="table" format="tabular" label="Table of Counts">
51 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.tabular" ext="tabular" visible="true" assign_primary_output="true" directory="outputdir"/> 56 <filter>output_option == "unique"</filter>
52 </data> 57 </data>
58
59 <collection name="split_output" type="list" label="Collection of Count Tables">
60 <filter>output_option == "multiple"</filter>
61 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.tabular" format="tabular" visible="false" directory="outputdir"/>
62 </collection>
63
53 </outputs> 64 </outputs>
54 <tests> 65 <tests>
55 <test> 66 <test expect_num_outputs="1">
56 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" /> 67 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
57 <param name="polarity" value="both" /> 68 <param name="polarity" value="both" />
58 <param name="output_option" value="unique" /> 69 <param name="output_option" value="unique" />
59 <output name="output" ftype="tabular" file="table.tabular" count="1"/> 70 <output name="table" ftype="tabular" file="table.tabular" count="1"/>
60 </test> 71 </test>
61 <test> 72 <test expect_num_outputs="1">
62 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" /> 73 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
63 <param name="polarity" value="both" /> 74 <param name="polarity" value="both" />
64 <param name="output_option" value="multiple" /> 75 <param name="output_option" value="multiple" />
65 <output name="output" ftype="tabular" file="table0.tabular"> 76 <output_collection name="split_output" type="list" count="2">
66 <discovered_dataset designation="table1" ftype="tabular" file="table1.tabular" /> 77 <element name="table0" file="table0.tabular" ftype="tabular" compare="contains" />
67 </output> 78 <element name="table1" file="table1.tabular" ftype="tabular" compare="contains" />
79 </output_collection>
68 </test> 80 </test>
69 <test> 81 <test expect_num_outputs="1">
70 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" /> 82 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
71 <param name="polarity" value="sense" /> 83 <param name="polarity" value="sense" />
72 <param name="output_option" value="unique" /> 84 <param name="output_option" value="unique" />
73 <output name="output" ftype="tabular" file="table.tabular" count="1"/> 85 <output name="table" ftype="tabular" file="table.tabular" count="1"/>
74 </test> 86 </test>
75 <test> 87 <test expect_num_outputs="1">
76 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" /> 88 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
77 <param name="polarity" value="antisense" /> 89 <param name="polarity" value="antisense" />
78 <param name="output_option" value="unique" /> 90 <param name="output_option" value="unique" />
79 <output name="output" ftype="tabular" file="table_antisense.tabular" count="1"/> 91 <output name="table" ftype="tabular" file="table_antisense.tabular" count="1"/>
80 </test> 92 </test>
81 93
82 <test> 94 <test expect_num_outputs="1">
83 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" /> 95 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
84 <param name="polarity" value="both" /> 96 <param name="polarity" value="both" />
85 <param name="output_option" value="multiple" /> 97 <param name="output_option" value="multiple" />
86 <output name="output" ftype="tabular" file="more_table0.tabular"> 98 <output_collection name="split_output" type="list" count="3">
87 <discovered_dataset designation="table1" ftype="tabular" file="more_table1.tabular" /> 99 <element name="table0" file="more_table0.tabular" ftype="tabular" compare="contains" />
88 <discovered_dataset designation="table2" ftype="tabular" file="more_table2.tabular" /> 100 <element name="table1" file="more_table1.tabular" ftype="tabular" compare="contains" />
89 </output> 101 <element name="table2" file="more_table2.tabular" ftype="tabular" compare="contains" />
102 </output_collection>
90 </test> 103 </test>
91 <test> 104 <test expect_num_outputs="1">
92 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" /> 105 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
93 <param name="polarity" value="sense" /> 106 <param name="polarity" value="sense" />
94 <param name="output_option" value="unique" /> 107 <param name="output_option" value="unique" />
95 <output name="output" ftype="tabular" file="more_sense_table.tabular" count="1"/> 108 <output name="table" ftype="tabular" file="more_sense_table.tabular" count="1"/>
96 </test> 109 </test>
97 <test> 110 <test expect_num_outputs="1">
98 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" /> 111 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
99 <param name="polarity" value="antisense" /> 112 <param name="polarity" value="antisense" />
100 <param name="output_option" value="unique" /> 113 <param name="output_option" value="unique" />
101 <output name="output" ftype="tabular" file="more_antisense_table.tabular" count="1"/> 114 <output name="table" ftype="tabular" file="more_antisense_table.tabular" count="1"/>
102 </test> 115 </test>
103
104
105 </tests> 116 </tests>
106 <help> 117 <help>
107 118
108 **What it does** 119 **What it does**
109 120