Mercurial > repos > galaxyp > spectrast2spectrast_irt
comparison spectrast2spectrast_irt.xml @ 0:7b3c4703d81a draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt commit d8b91dbe304c99bb5a46da25a5820005cde105c5-dirty
author | galaxyp |
---|---|
date | Sat, 30 May 2015 05:17:35 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:7b3c4703d81a |
---|---|
1 <tool id="gp_spectrast2spectrast_irt" name="SpectraST RT Normalizer" version="0.1.0"> | |
2 <description></description> | |
3 <requirements> | |
4 <requirement type="package" version="0.3.2">msproteomicstools</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <!-- Anything other than zero is an error --> | |
8 <exit_code range="1:" /> | |
9 <exit_code range=":-1" /> | |
10 <!-- In case the return code has not been set propery check stderr too --> | |
11 <regex match="Error:" /> | |
12 <regex match="Exception:" /> | |
13 </stdio> | |
14 <command> | |
15 <![CDATA[ | |
16 spectrast2spectrast_irt.py | |
17 --in ${input} | |
18 --out ./result_file.txt | |
19 #if str($kit) != 'None': | |
20 --kit "#echo ",".join(str($kit).split(','))#" | |
21 #end if | |
22 $applychauvenet | |
23 $precursorlevel | |
24 $spectralevel | |
25 $report | |
26 ##--exclude $exclude | |
27 ##--surrogate $surrogate | |
28 ##--linearregression $linearregression | |
29 --rsq_threshold $rsq_threshold | |
30 | |
31 ]]> | |
32 </command> | |
33 <inputs> | |
34 <param name="input" format="txt" type="data" label="Spectrast files" help="" /> | |
35 | |
36 <param name="applychauvenet" type="boolean" truevalue="--applychauvenet" falsevalue="" checked="False" | |
37 label="Use Chavenet's criterion to exclude outliers" help="(--applychauvenet)" /> | |
38 | |
39 <param name="precursorlevel" type="boolean" truevalue="--precursorlevel" falsevalue="" checked="False" | |
40 label="Use precursors instead of peptides for grouping" help="(--precursorlevel)" /> | |
41 | |
42 <param name="spectralevel" type="boolean" truevalue="--spectralevel" falsevalue="" checked="False" | |
43 label="Do not merge or group any peptides or precursors" help="Use raw spectra. (--spectralevel)" /> | |
44 | |
45 <param name="report" type="boolean" truevalue="--report" falsevalue="" checked="False" | |
46 label="Create a report CSV file" help="(--report)" /> | |
47 | |
48 <param name="rsq_threshold" type="float" value="0.95" label="Specify r-squared threshold to accept linear regression" help="(--rsq_threshold)" /> | |
49 | |
50 <param name="kit" type="select" multiple="True" optional="True" label="Specifiy RT-kit"> | |
51 <option value="LGGNEQVTR:-28.3083">LGGNEQVTR:-28.3083</option> | |
52 <option value="GAGSSEPVTGLDAK:0.227424">GAGSSEPVTGLDAK:0.227424</option> | |
53 <option value="VEATFGVDESNAK:13.1078">VEATFGVDESNAK:13.1078</option> | |
54 <option value="YILAGVENSK:22.3798">YILAGVENSK:22.3798</option> | |
55 <option value="TPVISGGPYEYR:28.9999">TPVISGGPYEYR:28.9999</option> | |
56 <option value="TPVITGAPYEYR:33.6311">TPVITGAPYEYR:33.6311</option> | |
57 <option value="DGLDAASYYAPVR:43.2819">DGLDAASYYAPVR:43.2819</option> | |
58 <option value="ADVTPADFSEWSK:54.969">ADVTPADFSEWSK:54.969</option> | |
59 <option value="GTFIIDPGGVIR:71.3819">GTFIIDPGGVIR:71.3819</option> | |
60 <option value="GTFIIDPAAVIR:86.7152">GTFIIDPAAVIR:86.7152</option> | |
61 <option value="LFLQFGAQGSPFLK:98.0897">LFLQFGAQGSPFLK:98.0897</option> | |
62 </param> | |
63 </inputs> | |
64 <outputs> | |
65 <data format="txt" from_work_dir="result_file.txt" name="output_splib" /> | |
66 <data format="txt" from_work_dir="result_file.pepidx" name="output_pepidx" /> | |
67 <data format="txt" from_work_dir="result_file.csv" name="output_report"> | |
68 <filter>report</filter> | |
69 </data> | |
70 </outputs> | |
71 <tests> | |
72 <!-- | |
73 <test> | |
74 <param name="input" value="HEK_Lib_7Nov13.splib" ftype="txt" /> | |
75 <param name="report" value="True" /> | |
76 <output name="output_splib" file="spectrast2spectrast_irt_output_1_splib.txt" ftype="txt" /> | |
77 <output name="output_pepidx" file="spectrast2spectrast_irt_output_1_pepids.txt" ftype="txt" /> | |
78 <output name="output_report" file="spectrast2spectrast_irt_output_1_report.txt" ftype="txt" /> | |
79 </test> | |
80 <test> | |
81 <param name="input" value="HEK_Lib_7Nov13.splib" ftype="txt" /> | |
82 <param name="report" value="False" /> | |
83 <param name="kit" value="LGGNEQVTR:-28.3083,GAGSSEPVTGLDAK:0.227424" /> | |
84 <output name="output_splib" file="spectrast2spectrast_irt_output_2_splib.txt" ftype="txt" /> | |
85 <output name="output_pepidx" file="spectrast2spectrast_irt_output_2_pepids.txt" ftype="txt" /> | |
86 </test> | |
87 --> | |
88 </tests> | |
89 <help> | |
90 <![CDATA[ | |
91 **What it does** | |
92 | |
93 Filter from spectraST files to swath input files. | |
94 | |
95 | |
96 ]]> | |
97 </help> | |
98 <citations> | |
99 </citations> | |
100 </tool> |