Mercurial > repos > lecorguille > xcms_retcor

annotate abims_xcms_retcor.xml @ 28:13885e67b123 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5f19510181ee5f15e2a2bee139c2cb2e6a5dd78e
author lecorguille
date Thu, 26 Oct 2017 11:16:24 -0400
parents 30410a052ab3
children c013ed353a2f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
1 <tool id="abims_xcms_retcor" name="xcms.retcor" version="2.2.0">
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
2
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
3 <description>Retention Time Correction using retcor function from xcms R package </description>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
4
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
5 <macros>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
6 <import>macros.xml</import>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
7 </macros>
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
8
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
9 <expand macro="requirements"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
10 <expand macro="stdio"/>
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
11
1
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
12 <command><![CDATA[
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
13 @COMMAND_XCMS_SCRIPT@
21
51b9f9452794 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4
lecorguille
parents: 18
diff changeset
14 image '$image'
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
15 xfunction retcor
1
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
16
21
51b9f9452794 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4
lecorguille
parents: 18
diff changeset
17 xsetRdataOutput '$xsetRData'
1
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
18
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
19 method $methods.method
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
20 #if $methods.method == "obiwarp":
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
21 profStep $methods.profStep
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
22 #else
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
23 smooth $methods.smooth
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
24 extra $methods.extra
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
25 missing $methods.missing
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
26 #if $methods.options.option == "show":
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
27 span $methods.options.span
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
28 family $methods.options.family
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
29 plottype $methods.options.plottype
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
30 #end if
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
31 #end if
10
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 9
diff changeset
32
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
33 @COMMAND_FILE_LOAD@
10
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 9
diff changeset
34
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
35 @COMMAND_LOG_EXIT@
1
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
36 ]]></command>
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
37
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
38 <inputs>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
39 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
40 <conditional name="methods">
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
41 <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" >
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
42 <option value="obiwarp" >obiwarp</option>
18
8e740205c907 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 717c02f887ce343ca55f862c8020aaf49f5581d8
lecorguille
parents: 16
diff changeset
43 <option value="peakgroups" selected="true">peakgroups</option>
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
44 </param>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
45 <when value="obiwarp">
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
46 <param name="profStep" type="float" value="1" label="Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files" />
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
47 </when>
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
48 <when value="peakgroups">
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
49 <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" >
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
50 <option value="loess">loess</option>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
51 <option value="linear">linear</option>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
52 </param>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
53 <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" />
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
54 <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" />
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
55
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
56 <conditional name="options">
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
57 <param name="option" type="select" label="Advanced options">
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
58 <option value="show">show</option>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
59 <option value="hide" selected="true">hide</option>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
60 </param>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
61 <when value="show">
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
62 <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/>
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
63
1
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
64 <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal">
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
65 <option value="gaussian" selected="true">gaussian</option>
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
66 <option value="symmetric">symmetric</option>
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
67 </param>
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
68
1
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
69 <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density">
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
70 <option value="none" selected="true">none</option>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
71 <option value="deviation">deviation</option>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
72 <option value="mdevden">mdevden</option>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
73 </param>
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
74
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
75 </when>
1
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
76 <when value="hide">
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
77 </when>
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
78 </conditional>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
79 </when>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
80 </conditional>
10
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 9
diff changeset
81
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
82 <expand macro="input_file_load"/>
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
83 <expand macro="input_tic_bpc_pdf"/>
10
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 9
diff changeset
84
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
85 </inputs>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
86
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
87 <outputs>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
88 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" />
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
89 <data name="rplotsPdf" format="pdf" from_work_dir="Rplots.pdf" label="${image.name[:-6]}.retcor.Rplots.pdf">
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
90 <filter>(methods['method'] == 'peakgroups')</filter>
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
91 <filter>(methods['options']['option'] == 'show')</filter>
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
92 <filter>(methods['options']['family'] == 'symmetric')</filter>
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
93 <filter>(methods['options']['plottype'] != 'none')</filter>
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
94 </data>
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
95 <data name="ticsCorPdf" format="pdf" from_work_dir="TICs.pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf">
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
96 <filter>tic_bpc_pdf</filter>
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
97 </data>
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
98 <data name="bpcsCorPdf" format="pdf" from_work_dir="BPCs.pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf">
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
99 <filter>tic_bpc_pdf</filter>
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
100 </data>
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
101 <collection name="ticsCorrectedTabCollection" type="list" label="TIC corrected tabular">
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
102 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
28
13885e67b123 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5f19510181ee5f15e2a2bee139c2cb2e6a5dd78e
lecorguille
parents: 27
diff changeset
103 <discover_datasets pattern="(?P&lt;designation&gt;.+)-TIC_corrected_mqc\.out" ext="tabular" />
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
104 </collection>
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
105 <collection name="bpcsCorrectedTabCollection" type="list" label="BPC corrected tabular">
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
106 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
28
13885e67b123 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5f19510181ee5f15e2a2bee139c2cb2e6a5dd78e
lecorguille
parents: 27
diff changeset
107 <discover_datasets pattern="(?P&lt;designation&gt;.+)-BPC_corrected_mqc\.out" ext="tabular" />
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
108 </collection>
1
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
109 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
110 </outputs>
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
111
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
112 <tests>
9
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
113 <!--<test>
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
114 <param name="image" value="xset.group.RData"/>
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
115 <param name="methods|method" value="peakgroups"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
116 <param name="methods|smooth" value="loess"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
117 <param name="methods|extra" value="1"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
118 <param name="methods|missing" value="1"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
119 <param name="methods|options|option" value="show"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
120 <param name="methods|options|span" value="0.2"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
121 <param name="methods|options|family" value="gaussian"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
122 <param name="methods|options|plottype" value="deviation"/>
10
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 9
diff changeset
123 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 9
diff changeset
124 <param name="zipfile_load_conditional|zip_file" value="sacuri_dir_root.zip" ftype="zip" />
1
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
125 <output name="log">
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
126 <assert_contents>
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
127 <has_text text="object with 4 samples" />
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
128 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
129 <has_text text="Mass range: 50.0021-999.9863 m/z" />
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
130 <has_text text="Peaks: 59359 (about 14840 per sample)" />
1
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
131 <has_text text="Peak Groups: 0" />
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
132 <has_text text="Sample classes: bio, blank" />
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
133 </assert_contents>
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
134 </output>
9
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
135 </test>-->
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
136 <test>
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
137 <param name="image" value="faahKO.xset.group.RData"/>
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
138 <expand macro="test_retcor_param"/>
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
139 <expand macro="test_file_load_zip"/>
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
140 <expand macro="test_retcor_output" raworcorrected="_corrected" />
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
141 </test>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
142 <test>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
143 <param name="image" value="faahKO-single-class.xset.group.RData"/>
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
144 <expand macro="test_retcor_param" />
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
145 <expand macro="test_file_load_single"/>
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
146 <expand macro="test_retcor_output" raworcorrected="_corrected" />
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
147 </test>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
148 </tests>
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
149
1
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
150 <help><![CDATA[
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
151
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
152 @HELP_AUTHORS@
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
153
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
154 ===========
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
155 Xcms.retcor
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
156 ===========
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
157
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
158 Description
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
159 -----------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
160
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
161 After matching peaks into groups, xcms can use those groups to identify and correct
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
162 correlated drifts in retention time from run to run. The aligned peaks can then be
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
163 used for a second pass of peak grouping which will be more accurate than the first.
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
164 The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
165 for identifying retention time drifts. Some groups may be missing peaks from a large
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
166 fraction of samples and thus provide an incomplete picture of the drift at that time point.
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
167 Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping.
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
168
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
169 .. class:: warningmark
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
170
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
171 **After an retcor step, it is mandatory to do a group step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
172 discarded)**
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
173
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
174
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
175
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
176 Workflow position
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
177 -----------------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
178
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
179
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
180 **Upstream tools**
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
181
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
182 +------------------------+------------------+--------------------+------------+
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
183 | Name | output file | format | parameter |
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
184 +========================+==================+====================+============+
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
185 | xcms.group | xset.group.RData | RData | RData file |
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
186 +------------------------+------------------+--------------------+------------+
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
187
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
188
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
189 **Downstream tools**
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
190
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
191 +---------------------------+------------------+--------+
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
192 | Name | Output file | Format |
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
193 +===========================+==================+========+
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
194 |xcms.group | xset.retcor.RData| RData |
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
195 +---------------------------+------------------+--------+
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
196
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
197 **General schema of the metabolomic workflow**
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
198
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
199 .. image:: xcms_retcor_workflow.png
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
200
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
201
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
202 ---------------------------------------------------
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
203
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
204 -----------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
205 Input files
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
206 -----------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
207
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
208 +---------------------------+----------------------+
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
209 | Parameter : num + label | Format |
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
210 +===========================+======================+
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
211 | 1 : RData file | rdata.xcms.group |
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
212 +---------------------------+----------------------+
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
213
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
214
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
215 ----------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
216 Parameters
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
217 ----------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
218
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
219 Method
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
220 ------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
221
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
222 **peakgroups**
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
223
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
224 | xcms ignores those groups by only considering well-behaved peak groups which are missing at most one sample and have at most one extra peak. (Those values can be changed with the **missing** and **extra** arguments.)
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
225 | For each of those well-behaved groups, the algorithm calculates a median retention time and, for every sample, a deviation from that median. Within a sample, the observed deviation generally changes over time in a nonlinear fashion. Those changes are approximated using a local polynomial regression technique implemented in the **loess** function. By default, the curve fitting is done using least-squares on all data points.
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
226 | However, it is possible to enable outlier detection and removal by setting the **family** argument to **symmetric**.
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
227
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
228 **obiwarp**
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
229
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
230 | Calculate retention time deviations for each sample using the obiwarp code at "http://obi-warp.sourceforge.net/". This function is able to align multiple samples by a center-star strategy. Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function. OBI-Warp harnesses the non-linear, comprehensive alignment power of DTW and builds on the discrete, non-bijective output of DTW to give natural interpolants that can be used across multiple datasets.
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
231 | For the original publication see :**Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpo-lated Warping John T. Prince and, Edward M. Marcotte Analytical Chemistry 2006 78 (17), 6140-6152.**
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
232
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
233
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
234 ------------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
235 Output files
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
236 ------------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
237
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
238 xset.group.retcor.RData: rdata.xcms.retcor format
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
239
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
240 | Rdata file that will be necessary in the **xcms.group** step of the workflow.
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
241
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
242 @HELP_BCP_TIC@
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
243
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
244
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
245 ---------------------------------------------------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
246
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
247 ---------------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
248 Working example
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
249 ---------------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
250
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
251 Input files
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
252 -----------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
253
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
254 | RData file -> **xset.group.RData**
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
255
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
256 Parameters
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
257 ----------
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
258
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
259 | **Method**: peakgroups
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
260 | **smooth**: loess
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
261 | **extra**: 1
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
262 | **missing**: 5
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
263 | **Advanced options**: show
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
264 | **span**: 0.4
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
265 | **family**: gaussian
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
266 | **plottype**: deviation
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
267
5
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
268
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
269 ---------------------------------------------------
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
270
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
271 Changelog/News
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
272 --------------
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
273
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
274 **Version 2.2.0 - 19/10/2017**
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
275
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
276 - NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC.
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 22
diff changeset
277
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
278 **Version 2.1.0 - 03/02/2017**
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
279
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
280 - IMPROVEMENT: xcms.retcor can deal with merged individual data
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
281
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
282 **Version 2.0.8 - 22/12/2016**
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
283
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
284 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
285
12
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
286 **Version 2.0.7 - 06/07/2016**
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
287
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
288 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
289
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
290 **Version 2.0.6 - 04/04/2016**
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
291
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
292 - TEST: refactoring to pass planemo test using conda dependencies
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
293
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
294
5
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
295 **Version 2.0.5 - 10/02/2016**
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
296
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
297 - BUGFIX: better management of errors. Datasets remained green although the process failed
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
298
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
299 - BUGFIX: some pdf remained empty even when the process succeed
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
300
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
301 - UPDATE: refactoring of internal management of inputs/outputs
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
302
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
303 - UPDATE: refactoring to feed the new report tool
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
304
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
305
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
306 **Version 2.0.2 - 02/06/2015**
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
307
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
308 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
309
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
310 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
311
d0efb2c07577 planemo upload
lecorguille
parents: 4
diff changeset
312
1
f42bd3de6aad Uploaded
lecorguille
parents: 0
diff changeset
313 ]]></help>
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
314
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
315
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
316 <expand macro="citation" />
0
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
317
ad95fea4015e planemo upload
lecorguille
parents:
diff changeset
318 </tool>