Mercurial > repos > tomnl > mspurity_flagremove

annotate flagRemove.xml @ 5:1a77ed3c94b7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 75d13d0237560528a1c6596a3ea5e327bed3e3a0
author tomnl
date Tue, 18 Jun 2019 10:39:15 -0400
parents 59c1f9077c3b
children b74303b60450
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
59c1f9077c3b planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 1
diff changeset
1 <tool id="mspurity_flagremove" name="msPurity.flagRemove" version="0.2.2">
0
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
2 <description>Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
3 (e.g. RSD of intensity and retention time).
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
4 </description>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
5
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
6 <macros>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
7 <import>macros.xml</import>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
8 </macros>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
9
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
10 <expand macro="requirements" />
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
11
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
12 <stdio>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
13 <exit_code range="1:" />
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
14 </stdio>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
15 <command interpreter="Rscript"><![CDATA[
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
16 flagRemove.R
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
17 --xset_path=$xset_path
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
18 --out_dir=.
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
19
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
20 #if $sample_flag.sample_flag=='update'
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
21 --rsd_i_sample=$sample_flag.rsd_i_sample
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
22 --minfrac_sample=$sample_flag.minfrac_sample
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
23 --ithres_sample=$sample_flag.ithres_sample
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
24 #end if
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
25
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
26 #if $blank_flag.blank_flag=='update'
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
27 --rsd_i_blank=$blank_flag.rsd_i_blank
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
28 --minfrac_blank=$blank_flag.minfrac_blank
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
29 --ithres_blank=$blank_flag.ithres_blank
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
30 --blank_class=$blank_flag.blank_class
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
31 #end if
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
32
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
33 #if $peak_removal.peak_removal=='remove'
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
34 --remove_spectra
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
35 --minfrac_xcms=$peak_removal.minfrac_xcms
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
36 --mzwid=$peak_removal.mzwid
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
37 --bw=$peak_removal.bw
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
38 #end if
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
39
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
40 #if $advanced.advanced=='update'
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
41 --egauss_thr=$advanced.egauss_thr
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
42 --polarity=$advanced.polarity
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
43 --grp_rm_ids=$advanced.grp_rm_ids
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
44 --xset_name=$advanced.xset_name
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
45 $advanced.temp_save.value
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
46
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
47 #end if
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
48 #if $choose_samp.choose_samp=='yes'
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
49 --samplelist=$choose_samp.samplelist
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
50 #end if
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
51 ]]></command>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
52 <inputs>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
53 <param type="data" name="xset_path" format='rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata'
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
54 help="The path to the xcmsSet object saved as an RData file"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
55 <conditional name="sample_flag">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
56 <param name="sample_flag" type="select" label="Change biological sample flag parameters?">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
57 <option value="update" >Update biological sample flag parameters</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
58 <option value="" selected="true">Use default biological sample flag parameters</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
59 </param>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
60 <when value="">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
61 </when>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
62 <when value="update">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
63 <param name="rsd_i_sample" type="text" label="rsd_i_sample" value="NA"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
64 help="Relative Standard Deviation threshold for the sample classes (--rsd_i_sample)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
65 <param name="minfrac_sample" type="float" label="minfrac_sample" value="0.5" min="0.0" max="1"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
66 help="minimum fraction of files for features needed for the sample classes (--minfrac_sample)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
67 <param name="rsd_rt_sample" type="text" label="rsd_rt_sample" value="NA"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
68 help="Relative standard Deviation threshold for the retention time of the sample
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
69 classes (--rsd_rt_sample)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
70 <param name="ithres_sample" type="text" label="ithres_sample" value="NA"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
71 help="Intensity threshold for the sample (--ithres_sample)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
72 </when>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
73 </conditional>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
74 <conditional name="blank_flag">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
75 <param name="blank_flag" type="select" label="Change blank flag parameters?">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
76 <option value="update" >Update blank flag parameters</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
77 <option value="" selected="true">Use default blank flag parameters</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
78 </param>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
79 <when value="">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
80 </when>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
81 <when value="update">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
82 <param name="blank_class" type="text" label="blank_class" value="blank"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
83 help="A string representing the class that will be used for the blank (--blank_class)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
84 <param name="rsd_i_blank" type="text" label="rsd_i_blank" value="NA"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
85 help="RSD threshold for the blank (--rsd_i_blank)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
86 <param name="minfrac_blank" type="float" label="minfrac_blank" value="0.5" min="0.0" max="1"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
87 help="minimum fraction of files for features needed for the blank (--minfrac_blank)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
88 <param name="rsd_rt_blank" type="text" label="rsd_rt_blank" value="NA"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
89 help="RSD threshold for the retention time of the blank (--rsd_rt_blank)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
90 <param name="ithres_blank" type="text" label="ithres_blank" value="NA"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
91 help="Intensity threshold for the blank (--ithres_blank)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
92 <param name="s2b" type="float" label="s2b" value="10"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
93 help="fold change (sample/blank) needed for sample peak to be allowed. e.g.
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
94 if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10.
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
95 1000/10 = 100, so sample has fold change higher than the threshold and the peak
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
96 is not considered a blank (--s2b)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
97 </when>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
98 </conditional>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
99 <conditional name="peak_removal">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
100 <param name="peak_removal" type="select" label="Remove peaks from xcmsSet object?">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
101 <option value="remove" >Remove peaks and re-group</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
102 <option value="" selected="true">Only flag peaks (do not remove and re-group)</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
103 </param>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
104 <when value="">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
105 </when>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
106 <when value="remove">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
107 <param name="minfrac_xcms" type="float" label="minfrac_xcms" value="0.7" min="0.0" max="1"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
108 help="minfrac for xcms grouping (--minfrac_xcms)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
109 <param name="mzwid" type="float" label="mzwid" value="0.001"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
110 help="mzwid for xcms grouping (--minfrac_xcms)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
111 <param name="bw" type="float" label="bw" value="5"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
112 help="bw for xcms grouping(--minfrac_xcms)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
113 </when>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
114 </conditional>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
115 <conditional name="advanced">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
116 <param name="advanced" type="select" label="Advanced parameters">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
117 <option value="update" >Update advanced and testing parameters</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
118 <option value="" selected="true">Use default advanced parameters</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
119 </param>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
120 <when value="">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
121 </when>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
122 <when value="update">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
123 <param name="egauss_thr" type="text" label="egauss_thr" value="NA"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
124 help="Threshold for filtering out non gaussian shaped peaks. Note this only works
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
125 if the 'verbose columns' and 'fit gauss' was used with xcms (--egauss_thr)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
126 <param name="temp_save" type="boolean" label="temp_save" checked="false" truevalue="--temp_save" falsevalue=""
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
127 help="Assign True if files for each step saved (for testing purposes) (--temp_save)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
128 <param name="polarity" type="select" label="polarity"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
129 help="polarity (just used for naming purpose when files are saved) (--polarity)">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
130 <option value="positive">Positive</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
131 <option value="negative" >Negative</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
132 <option value="NA" selected="true">NA</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
133 </param>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
134 <param name="grp_rm_ids" type="text" label="grp_rm_ids" value="NA"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
135 help="comma seperated list of grouped_xcms peak ids to remove (corresponds to the row from xcms::group output)
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
136 e.g '1,20,30,56'
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
137 (--grp_rm_ids)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
138 <param name="xset_name" type="text" label="xset_name" value="xset"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
139 help="Name of the xcmsSet object within the RData file (--xset_name)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
140 </when>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
141 </conditional>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
142 <conditional name="choose_samp">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
143 <param name="choose_samp" type="select" label="Samplelist">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
144 <option value="yes" >Use samplelist</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
145 <option value="" selected="true">Don't use samplelist</option>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
146 </param>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
147 <when value="">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
148 </when>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
149 <when value="yes">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
150 <param name="samplelist" type="data" label="samplelist" format="tsv,tabular"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
151 help="A samplelist can be provided to find an appriopiate blank class (requires a column 'blank' where 'yes' indicates the class should be used as the blank (--samplelist)"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
152
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
153 </when>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
154 </conditional>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
155 </inputs>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
156 <outputs>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
157 <data name="peaklist_filtered" format="tsv" label="${tool.name} on ${on_string}: peaklist_filtered (tsv)"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
158 from_work_dir="peaklist_filtered.tsv" />
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
159 <data name="removed_peaks" format="tsv" label="${tool.name} on ${on_string}: removed_peaks (tsv)"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
160 from_work_dir="removed_peaks.tsv" />
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
161 <data name="xset_filtered" format="rdata" label="xset_filtered"
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
162 from_work_dir="xset_filtered.RData"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
163 </outputs>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
164 <tests>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
165 <test>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
166 <param name="blank_flag.blank_flag" value="update" />
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
167 <param name="xset_path" value="flagRemove_input.RData"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
168
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
169 <param name="blank_flag.blank_flag" value="update" />
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
170 <conditional name="blank_flag">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
171 <param name="blank_flag" value="update"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
172 <param name="blank_class" value="KO" />
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
173 </conditional>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
174 <conditional name="peak_removal">
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
175 <param name="peak_removal" value="remove"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
176 </conditional>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
177 <output name="peaklist_filtered" file="flagRemove_output.tsv"/>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
178 </test>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
179 </tests>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
180 <help><![CDATA[
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
181
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
182 =======================================
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
183 Flag & remove peaks from xcmsSet object
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
184 =======================================
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
185 -----------
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
186 Description
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
187 -----------
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
188
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
189 Tool to flag XCMS grouped peaks based on various criteria (e.g RSD, intensity). The flagged grouped peaks can then be removed
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
190 completely from the xcmsSet object (xset). This means removing the individual peaks associated for each file. Located
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
191 in the **xset@peaks** socket of the xcmsSet object.
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
192
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
193 Additionally a list of ids of the xcms grouped peaks can be supplied, all peaks associated with these ids can be
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
194 be removed.
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
195
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
196 **Note**: grouped peak refers to a peak that has been grouped together by xcms::group function
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
197
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
198 -----------------
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
199 Updated peaklist
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
200 -----------------
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
201 The calculated columns for the update peaklist dataframe include:
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
202
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
203 * RSD of intensity for grouped peaks across each class
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
204 * RSD of retention time for grouped peaks across each class
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
205 * Coverage across all classes
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
206 * mzmin_full & mzmax_full: the full mzrange of each grouped peak
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
207 * rtmin_full & rtmax_full: the full rtrange of each grouped peak
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
208 * flag for criteria for the blank class (if 1 it means the blank is valid in at least 1 condition) and this grouped peak will be removed
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
209 * flag for criteria for the sample classes (if 1 it means that this grouped peak is valid for this class)
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
210 * all_sample_valid: flag for all samples (if 1 it means that at least 1 sample class is valid, this ignores the blank)
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
211
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
212 To filter out blank peaks just filter out all peaks where the blank_valid is equal to 1
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
213 This is in addition to the standard output from the xcmsSet peaklist
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
214
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
215 **flag example**
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
216
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
217 Dataset consists of 3 classes. Blank, cond1 and cond2. The classes cond1 and cond2 are biological sample classes.
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
218
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
219 ============= ============= ============= ================ ================
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
220 blank_valid cond1_valid cond2_valid all_sample_valid Keep peak?
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
221 ============= ============= ============= ================ ================
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
222 0 0 1 1 Yes
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
223 ------------- ------------- ------------- ---------------- ----------------
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
224 0 1 1 1 Yes
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
225 ------------- ------------- ------------- ---------------- ----------------
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
226 1 0 1 1 No
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
227 ------------- ------------- ------------- ---------------- ----------------
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
228 1 0 0 0 No
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
229 ------------- ------------- ------------- ---------------- ----------------
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
230 0 0 0 0 No
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
231 ============= ============= ============= ================ ================
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
232
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
233
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
234
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
235 -----------------
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
236 Filters for flags
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
237 -----------------
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
238
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
239 The following filters can be used to determine if a grouped peak gets flagged to keep. If the column all_sample_valid is 0 then
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
240 the grouped peak will be removed
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
241
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
242
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
243 * RSD of intensity for each biological sample class
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
244 * minfrac for each biological sample class
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
245 * RSD of retention time for each biological sample class
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
246 * intensity threshold for each biological sample class
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
247 * Blank subtraction. If a blank peak is found where the intensity of any corresponding biological sample class is not greater that the he s2b threshold (sample/blank). Then this grouped peak will be flagged for removal
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
248
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
249 The blank grouped peaks also have there own filters. If the blank peak passes this criteria and s2b threshold detailed above
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
250 then the peak will be removed.
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
251
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
252 * RSD of intensity
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
253 * minfrac
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
254 * intensity threshold
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
255
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
256 Additionally there is a filter for assessing how well the peaks fit the gaussian shape. Note that this can only be performed
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
257 when XCMS has fit_gauss option and verbose columns set to TRUE. Also, these peaks are just removed and not flagged.
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
258
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
259
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
260
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
261 -----------
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
262 Regrouping
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
263 -----------
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
264 The resulting xcmsSet object where all peaks have been removed needs to be regrouped otherwise the individual peaks
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
265 associated with each file will not be correctly linked to the grouped peaks.
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
266
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
267 This tool will re-group the xcmsSet object and check the newly created re-grouped xcmsSet object to see if any peaks are
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
268 still being flagged. If so the process will be repeated untill the xcmsSet object only contains peaks that match
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
269 the peak criteria.
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
270
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
271 The output file is an xcmsSet.RData file.
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
272 ]]></help>
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
273
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
274 <expand macro="citations" />
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
275 </tool>