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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse commit d520bdab019f9afc3f78912bfbd174909114da4f
author artbio
date Wed, 11 Oct 2023 01:59:32 +0000
parents 1997af8f4648
children
comparison
equal deleted inserted replaced
4:1997af8f4648 5:320f7746b9f5
1 <tool id="bamparse" name="Count alignments" version="4.1.0"> 1 <tool id="bamparse" name="Count alignments" version="4.1.1">
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>
65 <tests> 65 <tests>
66 <test expect_num_outputs="1"> 66 <test expect_num_outputs="1">
67 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" /> 67 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
68 <param name="polarity" value="both" /> 68 <param name="polarity" value="both" />
69 <param name="output_option" value="unique" /> 69 <param name="output_option" value="unique" />
70 <output name="table" ftype="tabular" file="table.tabular" count="1"/> 70 <output name="table" ftype="tabular" file="table.tabular" />
71 </test> 71 </test>
72 <test expect_num_outputs="1"> 72 <test expect_num_outputs="1">
73 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" /> 73 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
74 <param name="polarity" value="both" /> 74 <param name="polarity" value="both" />
75 <param name="output_option" value="multiple" /> 75 <param name="output_option" value="multiple" />
80 </test> 80 </test>
81 <test expect_num_outputs="1"> 81 <test expect_num_outputs="1">
82 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" /> 82 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
83 <param name="polarity" value="sense" /> 83 <param name="polarity" value="sense" />
84 <param name="output_option" value="unique" /> 84 <param name="output_option" value="unique" />
85 <output name="table" ftype="tabular" file="table.tabular" count="1"/> 85 <output name="table" ftype="tabular" file="table.tabular" />
86 </test> 86 </test>
87 <test expect_num_outputs="1"> 87 <test expect_num_outputs="1">
88 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" /> 88 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
89 <param name="polarity" value="antisense" /> 89 <param name="polarity" value="antisense" />
90 <param name="output_option" value="unique" /> 90 <param name="output_option" value="unique" />
91 <output name="table" ftype="tabular" file="table_antisense.tabular" count="1"/> 91 <output name="table" ftype="tabular" file="table_antisense.tabular" />
92 </test> 92 </test>
93 93
94 <test expect_num_outputs="1"> 94 <test expect_num_outputs="1">
95 <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" />
96 <param name="polarity" value="both" /> 96 <param name="polarity" value="both" />
103 </test> 103 </test>
104 <test expect_num_outputs="1"> 104 <test expect_num_outputs="1">
105 <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" />
106 <param name="polarity" value="sense" /> 106 <param name="polarity" value="sense" />
107 <param name="output_option" value="unique" /> 107 <param name="output_option" value="unique" />
108 <output name="table" ftype="tabular" file="more_sense_table.tabular" count="1"/> 108 <output name="table" ftype="tabular" file="more_sense_table.tabular" />
109 </test> 109 </test>
110 <test expect_num_outputs="1"> 110 <test expect_num_outputs="1">
111 <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" />
112 <param name="polarity" value="antisense" /> 112 <param name="polarity" value="antisense" />
113 <param name="output_option" value="unique" /> 113 <param name="output_option" value="unique" />
114 <output name="table" ftype="tabular" file="more_antisense_table.tabular" count="1"/> 114 <output name="table" ftype="tabular" file="more_antisense_table.tabular" />
115 </test> 115 </test>
116 </tests> 116 </tests>
117 <help> 117 <help>
118 118
119 **What it does** 119 **What it does**
124 Sense, antisense or both sense and antisense alignments can be counted 124 Sense, antisense or both sense and antisense alignments can be counted
125 125
126 The library labels in the returned count table are taken from the input bam datasets 126 The library labels in the returned count table are taken from the input bam datasets
127 names in the Galaxy history. 127 names in the Galaxy history.
128 </help> 128 </help>
129 <citations>
130 <citation type="doi">10.1093/bioinformatics/btp352</citation>
131 </citations>
129 </tool> 132 </tool>