Mercurial > repos > chrisd > testing

annotate gene_fraction.xml @ 3:bfd0aeb6030a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ChrisD11/Tools commit bf66a04a6b57ac86f2bd4794d3460698f4cbb8b7
author chrisd
date Mon, 22 Feb 2016 05:35:59 -0500
parents ed4a3695d6e8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
1 <tool id="gene_fraction" name="Coverage sampler" version="0.1.0">
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
2 <requirements>
3
bfd0aeb6030a planemo upload for repository https://github.com/ChrisD11/Tools commit bf66a04a6b57ac86f2bd4794d3460698f4cbb8b7
chrisd
parents: 2
diff changeset
3 <requirement type="package" version="0.1">csa</requirement>
0
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
4 </requirements>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
5 <stdio>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
6 <exit_code range="1:" />
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
7 </stdio>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
8 <command><![CDATA[
2
ed4a3695d6e8 planemo upload for repository https://github.com/ChrisD11/Tools commit d8d0247e1aa5fd1cb4108033430d044f165f5b2b
chrisd
parents: 0
diff changeset
9 csa
0
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
10 -amr_fp $input1
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
11 -sam_fp $input2
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
12 -min $min
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
13 -max $max
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
14 -t $threshold
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
15 -skip $skip
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
16 -samples $samples
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
17 -out_fp $output1
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
18 ]]></command>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
19 <inputs>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
20 <param type="data" name="input1" format="fasta" />
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
21 <param type="data" name="input2" format="sam" />
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
22 <param name="min" type="integer" label="Starting sample level"
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
23 value="1" min="1" max="100" help="(-min)" />
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
24 <param name="max" type="integer" label="Ending sample level"
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
25 value="1" min="1" max="100" help="(-max)" />
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
26 <param name="threshold" type="integer" label="Gene threshold"
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
27 value="1" min="1" max="100" help="(-t)" />
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
28 <param name="skip" type="integer" label="Amount of levels to skip"
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
29 value="1" min="1" max="100" help="(-skip)" />
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
30 <param name="samples" type="integer" label="Amount of samples per level"
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
31 value="1" min="1" max="100" help="(-samples)" />
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
32 </inputs>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
33 <outputs>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
34 <data name="output1" format="tabular" />
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
35 </outputs>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
36 <tests>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
37 <test>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
38 <param name="input1" value="ref.fa"/>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
39 <param name="input2" value="test.sam"/>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
40 <output name="outfil1" file="out.txt"/>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
41 </test>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
42 </tests>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
43 <help><![CDATA[
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
44
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
45 Program: Coverage Sampler
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
46 Contact: Chris Dean <cdean11@rams.colostate.edu
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
47
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
48 Usage: csa [options]
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
49
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
50 Options:
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
51
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
52 -amr_fp amr database path
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
53 -sam_fp sam file path
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
54 -min starting level
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
55 -max ending level
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
56 -skip amount of levels to skip
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
57 -t gene fraction threshold
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
58 -samples amount of samples per level
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
59 -d directory parsing
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
60 -bam bam file parsing
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
61 -out_fp output file path
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
62
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
63
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
64 ]]></help>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
65 </tool>