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comparison bamparse.xml @ 3:120eb76aa500 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
author artbio
date Mon, 17 Jul 2023 01:02:17 +0000
parents 8ea06787c08a
children 1997af8f4648
comparison
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2:8ea06787c08a 3:120eb76aa500
1 <tool id="bamparse" name="Count alignments" version="3.0.0"> 1 <tool id="bamparse" name="Count alignments" version="4.0.0">
2 <description>in a BAM file</description> 2 <description>in a BAM file</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.11.2.1">pysam</requirement> 4 <requirement type="package" version="0.21.0=py310h41dec4a_1">pysam</requirement>
5 <requirement type="package" version="0.6.6">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 </requirements> 7 </requirements>
7 <stdio> 8 <stdio>
8 <exit_code range="1:" level="fatal" description="Tool exception" /> 9 <exit_code range="1:" level="fatal" description="Tool exception" />
9 </stdio> 10 </stdio>
10 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
53 <tests> 54 <tests>
54 <test> 55 <test>
55 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" /> 56 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
56 <param name="polarity" value="both" /> 57 <param name="polarity" value="both" />
57 <param name="output_option" value="unique" /> 58 <param name="output_option" value="unique" />
58 <output name="output" ftype="tabular" file="table.tabular" /> 59 <output name="output" ftype="tabular" file="table.tabular" count="1"/>
59 </test> 60 </test>
60 <test> 61 <test>
61 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" /> 62 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
62 <param name="polarity" value="both" /> 63 <param name="polarity" value="both" />
63 <param name="output_option" value="multiple" /> 64 <param name="output_option" value="multiple" />
67 </test> 68 </test>
68 <test> 69 <test>
69 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" /> 70 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
70 <param name="polarity" value="sense" /> 71 <param name="polarity" value="sense" />
71 <param name="output_option" value="unique" /> 72 <param name="output_option" value="unique" />
72 <output name="output" ftype="tabular" file="table.tabular" /> 73 <output name="output" ftype="tabular" file="table.tabular" count="1"/>
73 </test> 74 </test>
74 <test> 75 <test>
75 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" /> 76 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
76 <param name="polarity" value="antisense" /> 77 <param name="polarity" value="antisense" />
77 <param name="output_option" value="unique" /> 78 <param name="output_option" value="unique" />
78 <output name="output" ftype="tabular" file="table_antisense.tabular" /> 79 <output name="output" ftype="tabular" file="table_antisense.tabular" count="1"/>
79 </test> 80 </test>
80 81
81 <test> 82 <test>
82 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" /> 83 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
83 <param name="polarity" value="both" /> 84 <param name="polarity" value="both" />
89 </test> 90 </test>
90 <test> 91 <test>
91 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" /> 92 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
92 <param name="polarity" value="sense" /> 93 <param name="polarity" value="sense" />
93 <param name="output_option" value="unique" /> 94 <param name="output_option" value="unique" />
94 <output name="output" ftype="tabular" file="more_sense_table.tabular" /> 95 <output name="output" ftype="tabular" file="more_sense_table.tabular" count="1"/>
95 </test> 96 </test>
96 <test> 97 <test>
97 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" /> 98 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
98 <param name="polarity" value="antisense" /> 99 <param name="polarity" value="antisense" />
99 <param name="output_option" value="unique" /> 100 <param name="output_option" value="unique" />
100 <output name="output" ftype="tabular" file="more_antisense_table.tabular" /> 101 <output name="output" ftype="tabular" file="more_antisense_table.tabular" count="1"/>
101 </test> 102 </test>
102 103
103 104
104 </tests> 105 </tests>
105 <help> 106 <help>