xcms_retcor: abims_xcms_retcor.xml annotate

annotate abims_xcms_retcor.xml @ 21:51b9f9452794 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4

author	lecorguille
date	Fri, 10 Feb 2017 11:02:38 -0500
parents	8e740205c907
children	411d2b9ea412

rev	line source
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	1 <tool id="abims_xcms_retcor" name="xcms.retcor" version="2.1.0">
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'
51b9f9452794 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 18 diff changeset	18 ticspdf '$ticsCorPdf'
51b9f9452794 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 18 diff changeset	19 bicspdf '$bpcsCorPdf'
51b9f9452794 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 18 diff changeset	20 rplotspdf '$rplotsPdf'
1 f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	21
f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	22 method $methods.method
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	23 #if $methods.method == "obiwarp":
ad95fea4015e planemo upload lecorguille parents: diff changeset	24 profStep $methods.profStep
ad95fea4015e planemo upload lecorguille parents: diff changeset	25 #else
ad95fea4015e planemo upload lecorguille parents: diff changeset	26 smooth $methods.smooth
ad95fea4015e planemo upload lecorguille parents: diff changeset	27 extra $methods.extra
ad95fea4015e planemo upload lecorguille parents: diff changeset	28 missing $methods.missing
ad95fea4015e planemo upload lecorguille parents: diff changeset	29 #if $methods.options.option == "show":
ad95fea4015e planemo upload lecorguille parents: diff changeset	30 span $methods.options.span
ad95fea4015e planemo upload lecorguille parents: diff changeset	31 family $methods.options.family
ad95fea4015e planemo upload lecorguille parents: diff changeset	32 plottype $methods.options.plottype
ad95fea4015e planemo upload lecorguille parents: diff changeset	33 #end if
ad95fea4015e planemo upload lecorguille parents: diff changeset	34 #end if
10 c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82 lecorguille parents: 9 diff changeset	35
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	36 @COMMAND_FILE_LOAD@
10 c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82 lecorguille parents: 9 diff changeset	37
14 55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 12 diff changeset	38 @COMMAND_LOG_EXIT@
1 f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	39 ]]></command>
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	40
ad95fea4015e planemo upload lecorguille parents: diff changeset	41 <inputs>
ad95fea4015e planemo upload lecorguille parents: diff changeset	42 <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	43 <conditional name="methods">
ad95fea4015e planemo upload lecorguille parents: diff changeset	44 <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	45 <option value="obiwarp" >obiwarp</option>
18 8e740205c907 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 717c02f887ce343ca55f862c8020aaf49f5581d8 lecorguille parents: 16 diff changeset	46 <option value="peakgroups" selected="true">peakgroups</option>
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	47 </param>
ad95fea4015e planemo upload lecorguille parents: diff changeset	48 <when value="obiwarp">
ad95fea4015e planemo upload lecorguille parents: diff changeset	49 <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	50 </when>
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 12 diff changeset	51 <when value="peakgroups">
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	52 <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	53 <option value="loess">loess</option>
ad95fea4015e planemo upload lecorguille parents: diff changeset	54 <option value="linear">linear</option>
ad95fea4015e planemo upload lecorguille parents: diff changeset	55 </param>
ad95fea4015e planemo upload lecorguille parents: diff changeset	56 <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	57 <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	58
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	59 <conditional name="options">
ad95fea4015e planemo upload lecorguille parents: diff changeset	60 <param name="option" type="select" label="Advanced options">
ad95fea4015e planemo upload lecorguille parents: diff changeset	61 <option value="show">show</option>
ad95fea4015e planemo upload lecorguille parents: diff changeset	62 <option value="hide" selected="true">hide</option>
ad95fea4015e planemo upload lecorguille parents: diff changeset	63 </param>
ad95fea4015e planemo upload lecorguille parents: diff changeset	64 <when value="show">
ad95fea4015e planemo upload lecorguille parents: diff changeset	65 <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	66
1 f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	67 <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	68 <option value="gaussian" selected="true">gaussian</option>
f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	69 <option value="symmetric">symmetric</option>
f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	70 </param>
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	71
1 f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	72 <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	73 <option value="none" selected="true">none</option>
ad95fea4015e planemo upload lecorguille parents: diff changeset	74 <option value="deviation">deviation</option>
ad95fea4015e planemo upload lecorguille parents: diff changeset	75 <option value="mdevden">mdevden</option>
ad95fea4015e planemo upload lecorguille parents: diff changeset	76 </param>
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	77
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	78 </when>
1 f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	79 <when value="hide">
f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	80 </when>
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	81 </conditional>
ad95fea4015e planemo upload lecorguille parents: diff changeset	82 </when>
ad95fea4015e planemo upload lecorguille parents: diff changeset	83 </conditional>
10 c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82 lecorguille parents: 9 diff changeset	84
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	85 <expand macro="file_load"/>
10 c7ae34138ee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82 lecorguille parents: 9 diff changeset	86
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	87 </inputs>
ad95fea4015e planemo upload lecorguille parents: diff changeset	88
ad95fea4015e planemo upload lecorguille parents: diff changeset	89 <outputs>
ad95fea4015e planemo upload lecorguille parents: diff changeset	90 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" />
ad95fea4015e planemo upload lecorguille parents: diff changeset	91 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.retcor.Rplots.pdf">
ad95fea4015e planemo upload lecorguille parents: diff changeset	92 <filter>(methods['method'] == 'peakgroups')</filter>
ad95fea4015e planemo upload lecorguille parents: diff changeset	93 <filter>(options['option'] == 'show')</filter>
ad95fea4015e planemo upload lecorguille parents: diff changeset	94 <filter>(family == 'symmetric')</filter>
ad95fea4015e planemo upload lecorguille parents: diff changeset	95 <filter>(plottype != 'none')</filter>
ad95fea4015e planemo upload lecorguille parents: diff changeset	96 </data>
ad95fea4015e planemo upload lecorguille parents: diff changeset	97 <data name="ticsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf" />
ad95fea4015e planemo upload lecorguille parents: diff changeset	98 <data name="bpcsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" />
1 f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	99 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	100 </outputs>
14 55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 12 diff changeset	101
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	102 <tests>
9 14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	103 <!--<test>
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	104 <param name="image" value="xset.group.RData"/>
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	105 <param name="methods\|method" value="peakgroups"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	106 <param name="methods\|smooth" value="loess"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	107 <param name="methods\|extra" value="1"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	108 <param name="methods\|missing" value="1"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	109 <param name="methods\|options\|option" value="show"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	110 <param name="methods\|options\|span" value="0.2"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	111 <param name="methods\|options\|family" value="gaussian"/>
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	112 <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	113 <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	114 <param name="zipfile_load_conditional\|zip_file" value="sacuri_dir_root.zip" ftype="zip" />
1 f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	115 <output name="log">
f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	116 <assert_contents>
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	117 <has_text text="object with 4 samples" />
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	118 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	119 <has_text text="Mass range: 50.0021-999.9863 m/z" />
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	120 <has_text text="Peaks: 59359 (about 14840 per sample)" />
1 f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	121 <has_text text="Peak Groups: 0" />
f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	122 <has_text text="Sample classes: bio, blank" />
f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	123 </assert_contents>
f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	124 </output>
9 14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	125 </test>-->
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	126 <test>
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	127 <param name="image" value="faahKO.xset.group.RData"/>
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	128 <param name="methods\|method" value="peakgroups"/>
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	129 <param name="methods\|smooth" value="loess"/>
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	130 <param name="methods\|extra" value="1"/>
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	131 <param name="methods\|missing" value="1"/>
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	132 <param name="methods\|options\|option" value="show"/>
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	133 <param name="methods\|options\|span" value="0.2"/>
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	134 <param name="methods\|options\|family" value="gaussian"/>
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	135 <param name="methods\|options\|plottype" value="deviation"/>
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	136 <param name="file_load_conditional\|file_load_select" value="yes" />
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	137 <param name="file_load_conditional\|inputs\|input" value="zip_file" />
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	138 <param name="file_load_conditional\|inputs\|zip_file" value="faahKO_reduce.zip" ftype="zip" />
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	139 <output name="log">
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	140 <assert_contents>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	141 <has_text text="object with 4 samples" />
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	142 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	143 <has_text text="Mass range: 200.1-600 m/z" />
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	144 <has_text text="Peaks: 9251 (about 2313 per sample)" />
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	145 <has_text text="Peak Groups: 0" />
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	146 <has_text text="Sample classes: KO, WT" />
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	147 </assert_contents>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	148 </output>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	149 </test>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	150 <test>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	151 <param name="image" value="faahKO-single-class.xset.group.RData"/>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	152 <param name="methods\|method" value="peakgroups"/>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	153 <param name="methods\|smooth" value="loess"/>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	154 <param name="methods\|extra" value="1"/>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	155 <param name="methods\|missing" value="1"/>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	156 <param name="methods\|options\|option" value="show"/>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	157 <param name="methods\|options\|span" value="0.2"/>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	158 <param name="methods\|options\|family" value="gaussian"/>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	159 <param name="methods\|options\|plottype" value="deviation"/>
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	160 <param name="file_load_conditional\|file_load_select" value="yes" />
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	161 <param name="file_load_conditional\|inputs\|input" value="single_file" />
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	162 <param name="file_load_conditional\|inputs\|single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
9 14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	163 <output name="log">
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	164 <assert_contents>
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	165 <has_text text="object with 4 samples" />
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	166 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	167 <has_text text="Mass range: 200.1-600 m/z" />
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	168 <has_text text="Peaks: 9251 (about 2313 per sample)" />
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	169 <has_text text="Peak Groups: 0" />
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	170 <has_text text="Sample classes: KO, WT" />
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	171 </assert_contents>
14242e316953 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	172 </output>
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	173 </test>
ad95fea4015e planemo upload lecorguille parents: diff changeset	174 </tests>
ad95fea4015e planemo upload lecorguille parents: diff changeset	175
1 f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	176 <help><![CDATA[
14 55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 12 diff changeset	177
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	178 @HELP_AUTHORS@
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	179
ad95fea4015e planemo upload lecorguille parents: diff changeset	180 ===========
ad95fea4015e planemo upload lecorguille parents: diff changeset	181 Xcms.retcor
ad95fea4015e planemo upload lecorguille parents: diff changeset	182 ===========
ad95fea4015e planemo upload lecorguille parents: diff changeset	183
ad95fea4015e planemo upload lecorguille parents: diff changeset	184 -----------
ad95fea4015e planemo upload lecorguille parents: diff changeset	185 Description
ad95fea4015e planemo upload lecorguille parents: diff changeset	186 -----------
ad95fea4015e planemo upload lecorguille parents: diff changeset	187
14 55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 12 diff changeset	188 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	189 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	190 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	191 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	192 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	193 fraction of samples and thus provide an incomplete picture of the drift at that time point.
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	194 Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping.
ad95fea4015e planemo upload lecorguille parents: diff changeset	195
ad95fea4015e planemo upload lecorguille parents: diff changeset	196 .. class:: warningmark
ad95fea4015e planemo upload lecorguille parents: diff changeset	197
ad95fea4015e planemo upload lecorguille parents: diff changeset	198 **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	199 discarded)**
ad95fea4015e planemo upload lecorguille parents: diff changeset	200
ad95fea4015e planemo upload lecorguille parents: diff changeset	201
ad95fea4015e planemo upload lecorguille parents: diff changeset	202
ad95fea4015e planemo upload lecorguille parents: diff changeset	203 -----------------
ad95fea4015e planemo upload lecorguille parents: diff changeset	204 Workflow position
ad95fea4015e planemo upload lecorguille parents: diff changeset	205 -----------------
ad95fea4015e planemo upload lecorguille parents: diff changeset	206
ad95fea4015e planemo upload lecorguille parents: diff changeset	207
ad95fea4015e planemo upload lecorguille parents: diff changeset	208 Upstream tools
ad95fea4015e planemo upload lecorguille parents: diff changeset	209
ad95fea4015e planemo upload lecorguille parents: diff changeset	210 ========================= ================= ======= ==========
ad95fea4015e planemo upload lecorguille parents: diff changeset	211 Name output file format parameter
ad95fea4015e planemo upload lecorguille parents: diff changeset	212 ========================= ================= ======= ==========
ad95fea4015e planemo upload lecorguille parents: diff changeset	213 xcms.group xset.group.RData RData RData file
ad95fea4015e planemo upload lecorguille parents: diff changeset	214 ========================= ================= ======= ==========
ad95fea4015e planemo upload lecorguille parents: diff changeset	215
ad95fea4015e planemo upload lecorguille parents: diff changeset	216
ad95fea4015e planemo upload lecorguille parents: diff changeset	217 Downstream tools
ad95fea4015e planemo upload lecorguille parents: diff changeset	218
ad95fea4015e planemo upload lecorguille parents: diff changeset	219 +---------------------------+------------------+--------+
ad95fea4015e planemo upload lecorguille parents: diff changeset	220 \| Name \| Output file \| Format \|
ad95fea4015e planemo upload lecorguille parents: diff changeset	221 +===========================+==================+========+
ad95fea4015e planemo upload lecorguille parents: diff changeset	222 \|xcms.group \| xset.retcor.RData\| RData \|
ad95fea4015e planemo upload lecorguille parents: diff changeset	223 +---------------------------+------------------+--------+
ad95fea4015e planemo upload lecorguille parents: diff changeset	224
ad95fea4015e planemo upload lecorguille parents: diff changeset	225 The output file xset.retcor.RData is an RData file. You can continue your analysis using it in xcms.group tool as an next step.
ad95fea4015e planemo upload lecorguille parents: diff changeset	226
ad95fea4015e planemo upload lecorguille parents: diff changeset	227
ad95fea4015e planemo upload lecorguille parents: diff changeset	228 General schema of the metabolomic workflow
ad95fea4015e planemo upload lecorguille parents: diff changeset	229
ad95fea4015e planemo upload lecorguille parents: diff changeset	230 .. image:: xcms_retcor_workflow.png
ad95fea4015e planemo upload lecorguille parents: diff changeset	231
ad95fea4015e planemo upload lecorguille parents: diff changeset	232
ad95fea4015e planemo upload lecorguille parents: diff changeset	233 -----------
ad95fea4015e planemo upload lecorguille parents: diff changeset	234 Input files
ad95fea4015e planemo upload lecorguille parents: diff changeset	235 -----------
ad95fea4015e planemo upload lecorguille parents: diff changeset	236
ad95fea4015e planemo upload lecorguille parents: diff changeset	237 +---------------------------+----------------------+
ad95fea4015e planemo upload lecorguille parents: diff changeset	238 \| Parameter : num + label \| Format \|
ad95fea4015e planemo upload lecorguille parents: diff changeset	239 +===========================+======================+
ad95fea4015e planemo upload lecorguille parents: diff changeset	240 \| 1 : RData file \| rdata.xcms.group \|
ad95fea4015e planemo upload lecorguille parents: diff changeset	241 +---------------------------+----------------------+
ad95fea4015e planemo upload lecorguille parents: diff changeset	242
ad95fea4015e planemo upload lecorguille parents: diff changeset	243
ad95fea4015e planemo upload lecorguille parents: diff changeset	244 ----------
ad95fea4015e planemo upload lecorguille parents: diff changeset	245 Parameters
ad95fea4015e planemo upload lecorguille parents: diff changeset	246 ----------
ad95fea4015e planemo upload lecorguille parents: diff changeset	247
ad95fea4015e planemo upload lecorguille parents: diff changeset	248 Method
ad95fea4015e planemo upload lecorguille parents: diff changeset	249 ------
ad95fea4015e planemo upload lecorguille parents: diff changeset	250
ad95fea4015e planemo upload lecorguille parents: diff changeset	251 peakgroups
ad95fea4015e planemo upload lecorguille parents: diff changeset	252
ad95fea4015e planemo upload lecorguille parents: diff changeset	253 \| 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	254 \| 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	255 \| However, it is possible to enable outlier detection and removal by setting the family argument to symmetric.
ad95fea4015e planemo upload lecorguille parents: diff changeset	256
ad95fea4015e planemo upload lecorguille parents: diff changeset	257 obiwarp
ad95fea4015e planemo upload lecorguille parents: diff changeset	258
ad95fea4015e planemo upload lecorguille parents: diff changeset	259 \| 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	260 \| 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	261
ad95fea4015e planemo upload lecorguille parents: diff changeset	262
ad95fea4015e planemo upload lecorguille parents: diff changeset	263 ------------
ad95fea4015e planemo upload lecorguille parents: diff changeset	264 Output files
ad95fea4015e planemo upload lecorguille parents: diff changeset	265 ------------
ad95fea4015e planemo upload lecorguille parents: diff changeset	266
ad95fea4015e planemo upload lecorguille parents: diff changeset	267 xset.group.retcor.TICs_corrected.pdf
ad95fea4015e planemo upload lecorguille parents: diff changeset	268
ad95fea4015e planemo upload lecorguille parents: diff changeset	269 \| "Total Ion Chromatograms" graph in pdf format,corrected after a retcor step.
ad95fea4015e planemo upload lecorguille parents: diff changeset	270
ad95fea4015e planemo upload lecorguille parents: diff changeset	271 xset.group.retcor.BPCs_corrected.pdf
ad95fea4015e planemo upload lecorguille parents: diff changeset	272
ad95fea4015e planemo upload lecorguille parents: diff changeset	273 \| "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step
ad95fea4015e planemo upload lecorguille parents: diff changeset	274
ad95fea4015e planemo upload lecorguille parents: diff changeset	275 xset.group.retcor.RData: rdata.xcms.retcor format
ad95fea4015e planemo upload lecorguille parents: diff changeset	276
ad95fea4015e planemo upload lecorguille parents: diff changeset	277 \| 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	278
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 12 diff changeset	279
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	280 ------
ad95fea4015e planemo upload lecorguille parents: diff changeset	281
14 55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 12 diff changeset	282 .. class:: infomark
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	283
ad95fea4015e planemo upload lecorguille parents: diff changeset	284 The output file is an xset.retcor.RData file. You can continue your analysis using it in xcms.fillPeaks tool.
ad95fea4015e planemo upload lecorguille parents: diff changeset	285
14 55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 12 diff changeset	286
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	287 ---------------------------------------------------
ad95fea4015e planemo upload lecorguille parents: diff changeset	288
ad95fea4015e planemo upload lecorguille parents: diff changeset	289 ---------------
ad95fea4015e planemo upload lecorguille parents: diff changeset	290 Working example
ad95fea4015e planemo upload lecorguille parents: diff changeset	291 ---------------
ad95fea4015e planemo upload lecorguille parents: diff changeset	292
ad95fea4015e planemo upload lecorguille parents: diff changeset	293 Input files
ad95fea4015e planemo upload lecorguille parents: diff changeset	294 -----------
ad95fea4015e planemo upload lecorguille parents: diff changeset	295
ad95fea4015e planemo upload lecorguille parents: diff changeset	296 \| RData file -> xset.group.RData
ad95fea4015e planemo upload lecorguille parents: diff changeset	297
ad95fea4015e planemo upload lecorguille parents: diff changeset	298 Parameters
ad95fea4015e planemo upload lecorguille parents: diff changeset	299 ----------
ad95fea4015e planemo upload lecorguille parents: diff changeset	300
ad95fea4015e planemo upload lecorguille parents: diff changeset	301 \| Method: -> peakgroups
ad95fea4015e planemo upload lecorguille parents: diff changeset	302 \| smooth: -> loess
ad95fea4015e planemo upload lecorguille parents: diff changeset	303 \| extra: -> 1
ad95fea4015e planemo upload lecorguille parents: diff changeset	304 \| missing -> 1
ad95fea4015e planemo upload lecorguille parents: diff changeset	305 \| Advanced options: -> show
ad95fea4015e planemo upload lecorguille parents: diff changeset	306 \| span -> 0.2
ad95fea4015e planemo upload lecorguille parents: diff changeset	307 \| family -> gaussian
ad95fea4015e planemo upload lecorguille parents: diff changeset	308 \| plottype -> deviation
14 55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 12 diff changeset	309
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	310
ad95fea4015e planemo upload lecorguille parents: diff changeset	311 Output files
ad95fea4015e planemo upload lecorguille parents: diff changeset	312 ------------
ad95fea4015e planemo upload lecorguille parents: diff changeset	313
ad95fea4015e planemo upload lecorguille parents: diff changeset	314 \| 1) xset.group.retcor.RData: RData file
ad95fea4015e planemo upload lecorguille parents: diff changeset	315
ad95fea4015e planemo upload lecorguille parents: diff changeset	316 \| 2) Example of an xset.group.retcor.TICs_corrected pdf file
ad95fea4015e planemo upload lecorguille parents: diff changeset	317
ad95fea4015e planemo upload lecorguille parents: diff changeset	318 .. image:: xcms_retcor.png
ad95fea4015e planemo upload lecorguille parents: diff changeset	319
5 d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	320
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	321 ---------------------------------------------------
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	322
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	323 Changelog/News
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	324 --------------
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	325
16 20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	326 Version 2.1.0 - 03/02/2017
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	327
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 14 diff changeset	328 - 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	329
14 55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 12 diff changeset	330 Version 2.0.8 - 22/12/2016
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 12 diff changeset	331
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 12 diff changeset	332 - 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	333
12 aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	334 Version 2.0.7 - 06/07/2016
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	335
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	336 - 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	337
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	338 Version 2.0.6 - 04/04/2016
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	339
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	340 - TEST: refactoring to pass planemo test using conda dependencies
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	341
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	342
5 d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	343 Version 2.0.5 - 10/02/2016
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	344
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	345 - BUGFIX: better management of errors. Datasets remained green although the process failed
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	346
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	347 - BUGFIX: some pdf remained empty even when the process succeed
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	348
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	349 - UPDATE: refactoring of internal management of inputs/outputs
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	350
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	351 - UPDATE: refactoring to feed the new report tool
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	352
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	353
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	354 Version 2.0.2 - 02/06/2015
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	355
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	356 - 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	357
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	358 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	359
d0efb2c07577 planemo upload lecorguille parents: 4 diff changeset	360
1 f42bd3de6aad Uploaded lecorguille parents: 0 diff changeset	361 ]]></help>
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	362
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	363
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	364 <expand macro="citation" />
0 ad95fea4015e planemo upload lecorguille parents: diff changeset	365
ad95fea4015e planemo upload lecorguille parents: diff changeset	366 </tool>

Mercurial > repos > lecorguille > xcms_retcor

annotate abims_xcms_retcor.xml @ 21:51b9f9452794 draft