Mercurial > repos > galaxyp > pyprophet_subsample

annotate pyprophet_subsample.xml @ 2:ca7b78db6af2 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/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
author galaxyp
date Tue, 14 Apr 2020 10:59:34 -0400
parents 973e601622a1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
1 <tool id="pyprophet_subsample" name="PyProphet subsample" version="@VERSION@.0">
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
2 <description>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
3 Subsample OpenSWATH file
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
4 </description>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
5 <macros>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
6 <import>macros.xml</import>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
7 </macros>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
8 <expand macro="requirements"/>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
9 <command detect_errors="aggressive">
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
10 <![CDATA[
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
11 pyprophet subsample
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
12 --in='$input'
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
13 --subsample_ratio=$subsample_ratio
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
14 $test_mode
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
15 --out='./output.osw'
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
16
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
17 ]]>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
18 </command>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
19 <inputs>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
20 <param name="input" type="data" format="osw" label="Input file" help="This file needs to be in OSW format." />
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
21 <param argument="--subsample_ratio" type="float" value="1" label="Subsample ratio used per input file (between 0 (0 %) and 1 (100 %))" />
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
22 <param name="test_mode" type="boolean" truevalue="--test" falsevalue="--no-test" label="Run in test mode with fixed seed" />
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
23 </inputs>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
24 <outputs>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
25 <data name="output" format="osw" label="${tool.name} on ${on_string}: subsample.osw" from_work_dir="output.osw" />
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
26 </outputs>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
27 <tests>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
28 <test>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
29 <param name="input" value="merged.osw" ftype="osw" />
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
30 <param name="subsample_ratio" value="0.5" />
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
31 <param name="test_mode" value="True" />
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
32 <output name="output" file="subsample.tabular" />
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
33 </test>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
34 </tests>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
35 <help>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
36 <![CDATA[
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
37 **What it does**
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
38
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
39 PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
40
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
41 Subsample OpenSWATH file to minimum for integrated scoring.
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
42
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
43 PyProphet is a Python re-implementation of the mProphet algorithm (Reiter 2010 Nature Methods) optimized for SWATH-MS data acquired by data-independent acquisition (DIA). The algorithm was originally published in (Telemann 2014 Bioinformatics) and has since been extended to support new data types and analysis modes (Rosenberger 2017, Nature biotechnology and Nature methods).
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
44
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
45 For more information, visit @link@
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
46
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
47 ]]>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
48 </help>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
49 <expand macro="citations"/>
973e601622a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
50 </tool>