annotate hardklor.xml @ 3:a979b9ff3272 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author galaxyp
date Wed, 07 Dec 2016 16:36:36 -0500
parents d796e6613d19
children 539f157784e7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
a979b9ff3272 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
1 <tool id="hardklor" name="Hardklor" version="2.30.1">
0
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
2 <description>identification of features from mass spectra</description>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
3 <requirements>
3
a979b9ff3272 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
4 <requirement type="package" version="2.3.0">hardklor</requirement>
0
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
5 </requirements>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
6 <stdio>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
7 <exit_code range="1:" level="fatal"/>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
8 </stdio>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
9 <command>python $__tool_directory__/hardklor.py "$ms1_in.extension" "$ms1_in"
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
10 "$output" -charge_algo=$cdm -resolution=$res -centroided=$centroided -instrument=$instrument -algorithm=$algorithm -mincharge=$chMin
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
11 -maxcharge=$chMax -mslvl=$mslvl -correlation=$corr -depth=$depth -sensitivity=$sens -maxfeat=$maxfeat</command>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
12 <inputs>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
13 <param name="ms1_in" type="data" format="mzml" label="MS1 files with precursor spectra " />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
14 <param name="res" type="integer" value="60000" label="Spectral resolution at 400m/z" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
15 <param name="centroided" type="select" display="radio" label="Centroided data?">
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
16 <option value="0" selected="true">No</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
17 <option value="1">Yes</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
18 </param>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
19 <param name="instrument" type="select" label="Instrument" >
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
20 <option value="Orbitrap" selected="true">Orbitrap</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
21 <option value="FTICR" >FTICR</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
22 <option value="TOF" >TOF</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
23 <option value="QIT" >Quadrupole ion trap</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
24 </param>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
25 <param name="mslvl" type="select" display="radio" label="MS level">
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
26 <option value="0" >All</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
27 <option value="1" selected="true">MS1</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
28 <option value="2">MS2</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
29 <option value="3">MS3</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
30 </param>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
31 <param name="algorithm" type="select" label="Algorithm">
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
32 <option value="Basic">Basic</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
33 <option value="Version1">Version 1</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
34 <option value="Version2" selected="true">Version 2</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
35 </param>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
36 <param name="cdm" type="select" label="Charge determination method">
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
37 <option value="None">None</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
38 <option value="FFT">Fast Fourier Transform</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
39 <option value="Patterson">Patterson Algorithm</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
40 <option value="Quick" selected="true">Quick</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
41 <option value="Senko">Senko</option>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
42 </param>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
43
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
44 <param name="chMin" type="integer" value="1" label="Min charge state" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
45 <param name="chMax" type="integer" value="5" label="Max charge state" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
46
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
47 <param name="corr" type="float" value="0.95" label="Correlation threshold" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
48 <param name="sens" type="integer" value="2" label="Sensitivity level" help="Ranges from 0 (min, fast) to 3 (max, slow)" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
49 <param name="depth" type="integer" value="2" label="Depth of combinatorial analysis"
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
50 help="Max number of overlapping features in any mz window. Keep as low as necessary for speed" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
51 <param name="maxfeat" type="integer" value="12" label="Max nr. of features for mz-window to solve" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
52
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
53 <!-- <param name="sn" type="float" value="1" label="Signal to noise threshold" help="Must be >=0" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
54 <param name="snWin" type="float" optional="true" label="Dynamic signal to noise window length (m/z)"
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
55 help="For spectra with varying noise levels (not for Thermo data)"/>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
56 <param name="win" type="float" value="5.25" label="Max width of any set of peaks in a spectrum" /> -->
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
57 </inputs>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
58
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
59 <outputs>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
60 <data format="hk" name="output" />
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
61 </outputs>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
62 <tests>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
63 <test>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
64 <param name="ms1_in" value="ms1_spectra.mzml"/>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
65 <output name="output" file="hardklor_result.hk"/>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
66 </test>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
67 </tests>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
68 <help>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
69 Hardklör identifies peptide or protein-like features in mass spectra. It deconvolves overlapping ion signals and can be used on a variety of input formats. The output of Hardklör can be used by the Krönik tool which summarizes the peptide features over time in an LC-MS experiment.
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
70 </help>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
71 <citations>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
72 <citation type="doi">10.1021/ac0700833</citation>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
73 <citation type="doi">10.1002/0471250953.bi1318s37</citation>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
74 </citations>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
galaxyp
parents:
diff changeset
75 </tool>