Mercurial > repos > chrisd > testing

annotate gene_fraction.xml @ 0:f95150c37d38 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 ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
author chrisd
date Sun, 21 Feb 2016 23:31:55 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f95150c37d38 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">
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
2 <requirements>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
3 </requirements>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
4 <stdio>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
5 <exit_code range="1:" />
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
6 </stdio>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
7 <command><![CDATA[
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
8 $__tool_directory__/csa
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
9 -amr_fp $input1
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
10 -sam_fp $input2
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
11 -min $min
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
12 -max $max
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
13 -t $threshold
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
14 -skip $skip
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
15 -samples $samples
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
16 -out_fp $output1
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
17 ]]></command>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
18 <inputs>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
19 <param type="data" name="input1" format="fasta" />
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
20 <param type="data" name="input2" format="sam" />
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
21 <param name="min" type="integer" label="Starting sample level"
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
22 value="1" min="1" max="100" help="(-min)" />
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
23 <param name="max" type="integer" label="Ending sample level"
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
24 value="1" min="1" max="100" help="(-max)" />
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
25 <param name="threshold" type="integer" label="Gene threshold"
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
26 value="1" min="1" max="100" help="(-t)" />
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
27 <param name="skip" type="integer" label="Amount of levels to skip"
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
28 value="1" min="1" max="100" help="(-skip)" />
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
29 <param name="samples" type="integer" label="Amount of samples per level"
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
30 value="1" min="1" max="100" help="(-samples)" />
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
31 </inputs>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
32 <outputs>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
33 <data name="output1" format="tabular" />
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
34 </outputs>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
35 <tests>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
36 <test>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
37 <param name="input1" value="ref.fa"/>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
38 <param name="input2" value="test.sam"/>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
39 <output name="outfil1" file="out.txt"/>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
40 </test>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
41 </tests>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
42 <help><![CDATA[
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
43
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
44 Program: Coverage Sampler
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
45 Contact: Chris Dean <cdean11@rams.colostate.edu
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
46
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
47 Usage: csa [options]
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
48
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
49 Options:
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
50
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
51 -amr_fp amr database path
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
52 -sam_fp sam file path
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
53 -min starting level
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
54 -max ending level
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
55 -skip amount of levels to skip
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
56 -t gene fraction threshold
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
57 -samples amount of samples per level
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
58 -d directory parsing
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
59 -bam bam file parsing
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
60 -out_fp output file path
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
61
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
62
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
63 ]]></help>
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
chrisd
parents:
diff changeset
64 </tool>