Mercurial > repos > chrisd > coverage_sampler

annotate coverage_sampler.xml @ 28:0669c68fadd5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit a9eb83d45f0260a8dbb8eff177412f4342c5899c-dirty
author chrisd
date Wed, 29 Jun 2016 03:48:35 -0400
parents 084c1b36be0d
children 5319e9db6473
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
284dec15f7f4 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 454f675c3a74cb7eb99f83ab3a299b82ec5f92b2-dirty
chrisd
parents: 9
diff changeset
1 <tool id="gene_fraction" name="Coverage Sampler" version="0.1.0">
6
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
2 <description>A simple tool for calculating the amount of a gene that is covered by a sample of alignments</description>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
3 <requirements>
12
284dec15f7f4 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 454f675c3a74cb7eb99f83ab3a299b82ec5f92b2-dirty
chrisd
parents: 9
diff changeset
4 <requirement type="package" version="0.1">coverage_sampler</requirement>
6
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
5 </requirements>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
6 <stdio>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
7 <exit_code range="1:" />
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
8 </stdio>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
9 <command><![CDATA[
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
10 csa
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
11 -ref_fp $reference
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
12 -sam_fp $sam
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
13 -min $min
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
14 -max $max
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
15 -t $threshold
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
16 -skip $skip
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
17 -samples $samples
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
18 -out_fp $output
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
19 ]]></command>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
20 <inputs>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
21 <param type="data" name="reference" format="fasta" label="Reference sequence" />
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
22 <param type="data" name="sam" format="sam" label="SAM file" />
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
23 <param name="min" type="integer" label="Starting sample level"
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
24 value="1" min="1" max="100" help="(-min)" />
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
25 <param name="max" type="integer" label="Ending sample level"
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
26 value="1" min="1" max="100" help="(-max)" />
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
27 <param name="threshold" type="integer" label="Gene fraction threshold"
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
28 value="0" min="0" max="100" help="(-t)" />
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
29 <param name="skip" type="integer" label="Amount of sample levels to skip"
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
30 value="1" min="1" max="100" help="(-skip)" />
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
31 <param name="samples" type="integer" label="Iterations per sample level"
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
32 value="1" min="1" max="100" help="(-samples)" />
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
33 </inputs>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
34 <outputs>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
35 <data name="output" format="tabular" />
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
36 </outputs>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
37 <tests>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
38 <test>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
39 <param name="reference" value="ref.fa"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
40 <param name="sam" value="sampe.sam"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
41 <param name="min" value="100"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
42 <param name="max" value="100"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
43 <param name="threshold" value="50"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
44 <param name="skip" value="5"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
45 <param name="samples" value="1"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
46 <output name="output" file="csa_result" ftype="tabular"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
47 </test>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
48 <test>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
49 <param name="reference" value="ref.fa"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
50 <param name="sam" value="sampe.sam"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
51 <param name="min" value="100"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
52 <param name="max" value="100"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
53 <param name="threshold" value="80"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
54 <param name="skip" value="5"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
55 <param name="samples" value="1"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
56 <output name="output" file="csa_no_result" ftype="tabular"/>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
57 </test>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
58 </tests>
14
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
59 <help>
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
60 <![CDATA[
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
61
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
62 **Coverage sampler**
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
63
15
233b2d979df4 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 98296c46d15c170e77d5eefad61cc447378fa73a-dirty
chrisd
parents: 14
diff changeset
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
14
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
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
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
66 that was covered from a random sampling of alignments.
6
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
67
14
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
68 ------
6
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
69
14
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
70 **Options**
6
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
71
26
89c934705f57 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 8f733c58a6f788a3bb453090601a2f7e22f1f9ae-dirty
chrisd
parents: 25
diff changeset
72 -min INT Starting level to sample reads from (level is in percent)
25
99d75ed267fd planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 4bed44dc2dcea45acef8693ccd6fbd7aee51aacd-dirty
chrisd
parents: 24
diff changeset
73 -max INT Ending level to sample reads from (level is in percent)
99d75ed267fd planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 4bed44dc2dcea45acef8693ccd6fbd7aee51aacd-dirty
chrisd
parents: 24
diff changeset
74 -skip INT Number of levels to skip
99d75ed267fd planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 4bed44dc2dcea45acef8693ccd6fbd7aee51aacd-dirty
chrisd
parents: 24
diff changeset
75 -t INT Gene fraction threshold (only genes with a gene fraction greater than this threshold are output)
99d75ed267fd planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 4bed44dc2dcea45acef8693ccd6fbd7aee51aacd-dirty
chrisd
parents: 24
diff changeset
76 -samples INT Number of iterations per sample level
28
0669c68fadd5 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit a9eb83d45f0260a8dbb8eff177412f4342c5899c-dirty
chrisd
parents: 27
diff changeset
77
0669c68fadd5 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit a9eb83d45f0260a8dbb8eff177412f4342c5899c-dirty
chrisd
parents: 27
diff changeset
78
14
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
79 ------
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
80
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
81 **Output**
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
82
15
233b2d979df4 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 98296c46d15c170e77d5eefad61cc447378fa73a-dirty
chrisd
parents: 14
diff changeset
83 Output of this program is a tab delimited text file with following:
14
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
84
24
750a09c9cca2 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit b3a650c3506c27e7b80069dd88d87fa11c5369b9-dirty
chrisd
parents: 23
diff changeset
85 Column Description
25
99d75ed267fd planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 4bed44dc2dcea45acef8693ccd6fbd7aee51aacd-dirty
chrisd
parents: 24
diff changeset
86 Level The sampling level alignments were taken at
24
750a09c9cca2 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit b3a650c3506c27e7b80069dd88d87fa11c5369b9-dirty
chrisd
parents: 23
diff changeset
87 Iteration The ith iteration of the current sampling level
25
99d75ed267fd planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 4bed44dc2dcea45acef8693ccd6fbd7aee51aacd-dirty
chrisd
parents: 24
diff changeset
88 Gene Id The reference sequence having a gene fraction greater than threshold
24
750a09c9cca2 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit b3a650c3506c27e7b80069dd88d87fa11c5369b9-dirty
chrisd
parents: 23
diff changeset
89 Gene Fraction The overall fraction of the gene that was covered from the sample of alignments
25
99d75ed267fd planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 4bed44dc2dcea45acef8693ccd6fbd7aee51aacd-dirty
chrisd
parents: 24
diff changeset
90 Hits The amount of times that the reference sequence was seen from the sample of alignments
14
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
91
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
92 ------
53a59e1eaa73 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit deb65bbedf931660e614f8fbffe0567d03c5a133-dirty
chrisd
parents: 12
diff changeset
93
15
233b2d979df4 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 98296c46d15c170e77d5eefad61cc447378fa73a-dirty
chrisd
parents: 14
diff changeset
94 **Development**
233b2d979df4 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 98296c46d15c170e77d5eefad61cc447378fa73a-dirty
chrisd
parents: 14
diff changeset
95
233b2d979df4 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 98296c46d15c170e77d5eefad61cc447378fa73a-dirty
chrisd
parents: 14
diff changeset
96 Development is being done on github_
233b2d979df4 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 98296c46d15c170e77d5eefad61cc447378fa73a-dirty
chrisd
parents: 14
diff changeset
97
233b2d979df4 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 98296c46d15c170e77d5eefad61cc447378fa73a-dirty
chrisd
parents: 14
diff changeset
98 .. _github: https://github.com/cdeanj/coverage_sampler
233b2d979df4 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 98296c46d15c170e77d5eefad61cc447378fa73a-dirty
chrisd
parents: 14
diff changeset
99
25
99d75ed267fd planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 4bed44dc2dcea45acef8693ccd6fbd7aee51aacd-dirty
chrisd
parents: 24
diff changeset
100 ]]></help>
6
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
101 <citations>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
102 </citations>
59c6a5729ce0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
chrisd
parents:
diff changeset
103 </tool>