Mercurial > repos > chrisd > coverage_sampler
comparison coverage_sampler.xml @ 32:8998b3f44018 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit f40bbce10577e858968aede35464f9c6cb5b2a95-dirty
| author | chrisd |
|---|---|
| date | Wed, 29 Jun 2016 03:58:04 -0400 |
| parents | 9b2f98681608 |
| children | fab5cf882885 |
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| 31:9b2f98681608 | 32:8998b3f44018 |
|---|---|
| 54 <param name="skip" value="5"/> | 54 <param name="skip" value="5"/> |
| 55 <param name="samples" value="1"/> | 55 <param name="samples" value="1"/> |
| 56 <output name="output" file="csa_no_result" ftype="tabular"/> | 56 <output name="output" file="csa_no_result" ftype="tabular"/> |
| 57 </test> | 57 </test> |
| 58 </tests> | 58 </tests> |
| 59 <help> | 59 <help><![CDATA[ |
| 60 <![CDATA[ | |
| 61 | 60 |
| 62 **Coverage sampler** | 61 **Coverage sampler** |
| 63 | 62 |
| 64 Coverage sampler is a simple tool for calculating the amount of a gene that is covered by a sample of alignments. The tool takes | 63 Coverage sampler is a simple tool for calculating the amount of a gene that is covered by a sample of alignments. The tool takes |
| 65 in as input a fasta and alignment file. The output of this program is a tab delimited text file describing the fraction of each gene | 64 in as input a fasta and alignment file. The output of this program is a tab delimited text file describing the fraction of each gene |
| 68 ------ | 67 ------ |
| 69 | 68 |
| 70 **Options** | 69 **Options** |
| 71 | 70 |
| 72 -min INT Starting level to sample reads from (level is in percent) | 71 -min INT Starting level to sample reads from (level is in percent) |
| 72 | |
| 73 -max INT Ending level to sample reads from (level is in percent) | 73 -max INT Ending level to sample reads from (level is in percent) |
| 74 | |
| 74 -skip INT Number of levels to skip | 75 -skip INT Number of levels to skip |
| 76 | |
| 75 -samples INT Number of iterations per sample level | 77 -samples INT Number of iterations per sample level |
| 78 | |
| 76 -t INT Gene fraction threshold (only genes with a gene fraction greater than this threshold are output) | 79 -t INT Gene fraction threshold (only genes with a gene fraction greater than this threshold are output) |
| 77 | 80 |
| 78 ------ | 81 ------ |
| 79 | 82 |
| 80 **Output** | 83 **Output** |