Mercurial > repos > chrisd > coverage_sampler
comparison coverage_sampler.xml @ 14:53a59e1eaa73 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
| author | chrisd |
|---|---|
| date | Wed, 29 Jun 2016 02:33:49 -0400 |
| parents | 284dec15f7f4 |
| children | 233b2d979df4 |
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| 13:65d8343a6122 | 14:53a59e1eaa73 |
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| 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><![CDATA[ | 59 <help> |
| 60 A simple tool for calculating the amount of a gene that is covered by a sample of alignments. | 60 <![CDATA[ |
| 61 | 61 |
| 62 Program: Coverage Sampler | 62 **Coverage sampler** |
| 63 | 63 |
| 64 Contact: Chris Dean <cdean11@rams.colostate.edu> | 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 |
| 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 | |
| 66 that was covered from a random sampling of alignments. | |
| 65 | 67 |
| 66 Usage: csa [options] | 68 .. _Coverage sampler: https://github.com/cdeanj/coverage_sampler |
| 67 | 69 |
| 68 Options: | 70 ------ |
| 69 -ref_fp STR/FILE ref file path | 71 |
| 70 -sam_fp STR/FILE sam file path | 72 **Options** |
| 71 -min INT starting sample level | 73 |
| 72 -max INT ending sample level | 74 -min This parameter specifies the starting sample level for the program. For example, a min value |
| 73 -skip INT amount of sample levels to skip | 75 of five tells the program to begin by taking five percent of alignments from the alignment file. |
| 74 -t INT gene fraction threshold | 76 |
| 75 -samples INT iterations per sample level | 77 -max This parameter specifies the ending sample level for the program. |
| 76 -out_fp STR/FILE output file path | 78 |
| 77 ]]></help> | 79 -skip This parameter specifies the amount of levels to skip between min and max. For example, |
| 80 if you specify a min value of five, a max value of 100, and a skip value of five, then | |
| 81 you would be sampling alignments in intervals of five. | |
| 82 | |
| 83 -t This parameter specifies a threshold value. Only genes having a gene fraction greater than | |
| 84 this value are provided as output. | |
| 85 | |
| 86 -samples This parameter specifies the amount of iterations you would like to sample at. For example, a | |
| 87 sample value of five would sample each level five times. | |
| 88 | |
| 89 ------ | |
| 90 | |
| 91 **Output** | |
| 92 | |
| 93 Output of this program is a tab delimited text file with following: | |
| 94 | |
| 95 1 Level The sampling level alignments were taken at | |
| 96 2 Iteration The ith iteration of the current sampling level | |
| 97 3 Gene Id The reference sequence having a gene fraction greater than threshold | |
| 98 4 Gene Fraction The overall fraction of the gene that was covered from the sample of alignments | |
| 99 5 Hits The amount of times that the reference sequence was seen from the sample of alignments | |
| 100 | |
| 101 ------ | |
| 102 | |
| 103 ]]> | |
| 104 </help> | |
| 78 <citations> | 105 <citations> |
| 79 </citations> | 106 </citations> |
| 80 </tool> | 107 </tool> |