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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 9982b8cd32dc6ecef17cd8c3bf16f42d8eb30d75-dirty
author chrisd
date Thu, 30 Jun 2016 02:15:50 -0400
parents fa1aae53a2f3
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1:fa1aae53a2f3 2:ec439b0e7512
1 <tool id="gene_fraction" name="Coverage Sampler" version="0.1.0"> 1 <tool id="gene_fraction" name="Coverage Sampler" version="0.1.0">
2 <description>A simple tool for calculating the amount of a gene that is covered by a sample of alignments</description> 2 <description>A simple tool for calculating the amount of a gene that is covered by a sample of alignments</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1">csa</requirement> 4 <requirement type="package" version="0.1">coverage_sampler</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 <command><![CDATA[ 9 <command><![CDATA[
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><![CDATA[
60 A simple tool for calculating the amount of a gene that is covered by a sample of alignments.
61 60
62 Program: Coverage Sampler 61 **Coverage sampler**
63 62
64 Contact: Chris Dean <cdean11@rams.colostate.edu> 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
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
65 that was covered from a random sampling of alignments.
65 66
66 Usage: csa [options] 67 ------
67 68
68 Options: 69 **Options**
69 -ref_fp STR/FILE ref file path 70
70 -sam_fp STR/FILE sam file path 71 -min INT Starting level to sample reads from (level is in percent)
71 -min INT starting sample level 72
72 -max INT ending sample level 73 -max INT Ending level to sample reads from (level is in percent)
73 -skip INT amount of sample levels to skip 74
74 -t INT gene fraction threshold 75 -skip INT Number of levels to skip
75 -samples INT iterations per sample level 76
76 -out_fp STR/FILE output file path 77 -samples INT Number of iterations per sample level
77 ]]></help> 78
79 -t INT Gene fraction threshold (only genes with a gene fraction greater than this threshold are output)
80
81 ------
82
83 **Output**
84
85 A tab delimited text file with the following columns::
86
87 Level The sampling level alignments were taken at
88 Iteration The iteration number of the current sample level
89 Gene Id The reference name having a gene fraction greater than threshold
90 Gene Fraction The gene fraction for the current reference sequence (in percent)
91 Hits The number of alignments associated with the reference sequence
92
93 ------
94
95 **Development**
96
97 Development is being done on github_
98
99 .. _github: https://github.com/cdeanj/coverage_sampler
100
101 ]]></help>
78 <citations> 102 <citations>
79 </citations> 103 </citations>
80 </tool> 104 </tool>