Mercurial > repos > artbio > bamparse
comparison bamparse.xml @ 5:320f7746b9f5 draft default tip
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 |
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| 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> |