xcms_group: abims_xcms_group.xml annotate

annotate abims_xcms_group.xml @ 27:36b470f3ebcf draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9

author	lecorguille
date	Tue, 24 Oct 2017 11:47:07 -0400
parents	e121f6d76dfb
children	a18fc7554c6d

rev	line source
19 7f667b64d5a5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 17 diff changeset	1 <tool id="abims_xcms_group" name="xcms.group" version="2.1.0">
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	2
2a104ea58d12 Uploaded lecorguille parents: diff changeset	3 <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	4
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	5 <macros>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	6 <import>macros.xml</import>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	7 </macros>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	8
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	9 <expand macro="requirements"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	10 <expand macro="stdio"/>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	11
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	12 <command><![CDATA[
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	13 @COMMAND_XCMS_SCRIPT@
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	14 xfunction group
19 7f667b64d5a5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 17 diff changeset	15 image '$image'
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	16
19 7f667b64d5a5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 17 diff changeset	17 xsetRdataOutput '$xsetRData'
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	18
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	19 method $methods.method
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	20 #if $methods.method == "density":
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	21 ## minsamp $methods.minsamp
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	22 minfrac $methods.minfrac
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	23 bw $methods.bw
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	24 mzwid $methods.mzwid
26 e121f6d76dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a0206fe6932fda018ecd078134d884aec36aeb97 lecorguille parents: 24 diff changeset	25 sleep 0.001
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	26 #if $methods.density_options.option == "show":
2a104ea58d12 Uploaded lecorguille parents: diff changeset	27 max $methods.density_options.max
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	28 #end if
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	29 #elif $methods.method == "mzClust":
2a104ea58d12 Uploaded lecorguille parents: diff changeset	30 mzppm $methods.mzppm
2a104ea58d12 Uploaded lecorguille parents: diff changeset	31 mzabs $methods.mzabs
2a104ea58d12 Uploaded lecorguille parents: diff changeset	32 minfrac $methods.minfrac
2a104ea58d12 Uploaded lecorguille parents: diff changeset	33 ## minsamp $methods.minsamp
2a104ea58d12 Uploaded lecorguille parents: diff changeset	34 #else:
2a104ea58d12 Uploaded lecorguille parents: diff changeset	35 mzVsRTbalance $methods.mzVsRTbalance
2a104ea58d12 Uploaded lecorguille parents: diff changeset	36 mzCheck $methods.mzCheck
2a104ea58d12 Uploaded lecorguille parents: diff changeset	37 rtCheck $methods.rtCheck
2a104ea58d12 Uploaded lecorguille parents: diff changeset	38 kNN $methods.kNN
2a104ea58d12 Uploaded lecorguille parents: diff changeset	39 #end if
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	40
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	41 @COMMAND_PEAKLIST@
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	42
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	43 @COMMAND_LOG_EXIT@
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	44 ]]></command>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	45
2a104ea58d12 Uploaded lecorguille parents: diff changeset	46 <inputs>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	47 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
2a104ea58d12 Uploaded lecorguille parents: diff changeset	48 <conditional name="methods">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	49 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	50 <option value="density" selected="true">density</option>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	51 <option value="mzClust" >mzClust</option>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	52 <option value="nearest" >nearest</option>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	53 </param>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	54 <when value="density">
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	55 <param name="bw" type="float" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	56 <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" />
2a104ea58d12 Uploaded lecorguille parents: diff changeset	57 <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " />
2a104ea58d12 Uploaded lecorguille parents: diff changeset	58 <!--
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	59 <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	60 -->
2a104ea58d12 Uploaded lecorguille parents: diff changeset	61 <conditional name="density_options">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	62 <param name="option" type="select" label="Advanced options">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	63 <option value="show">show</option>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	64 <option value="hide" selected="true">hide</option>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	65 </param>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	66 <when value="show">
22 b41669de74ae planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 19 diff changeset	67 <param name="max" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" help="[max]" />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	68 </when>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	69 <when value="hide">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	70 </when>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	71 </conditional>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	72
2a104ea58d12 Uploaded lecorguille parents: diff changeset	73 </when>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	74 <when value="mzClust">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	75 <param name="mzppm" type="integer" value="20 " label="Relative error used for clustering/grouping in ppm" help="[mzppm]" />
2a104ea58d12 Uploaded lecorguille parents: diff changeset	76 <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" />
2a104ea58d12 Uploaded lecorguille parents: diff changeset	77 <param name="minfrac" type="float" value="0" label="Minimum fraction of each class in one bin" help="[minfrac] minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group" />
2a104ea58d12 Uploaded lecorguille parents: diff changeset	78 <!--
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	79 <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	80 -->
2a104ea58d12 Uploaded lecorguille parents: diff changeset	81 </when>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	82 <when value="nearest">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	83 <param name="mzVsRTbalance" type="integer" value="10 " label="Multiplicator for mz value before calculating the (euclidean) distance between two peaks." help="[mzVsRTbalance]" />
2a104ea58d12 Uploaded lecorguille parents: diff changeset	84 <param name="mzCheck" type="float" value="0.2" label="Maximum tolerated distance for mz" help="[mzCheck]" />
2a104ea58d12 Uploaded lecorguille parents: diff changeset	85 <param name="rtCheck" type="integer" value="15" label="Maximum tolerated distance for RT" help="[rtCheck]" />
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	86 <param name="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" help="[kNN]" />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	87 </when>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	88 </conditional>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	89 <!--
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	90 <param name="sleepy" type="float" value="0.001" label="sleep" help="seconds to pause between plotting successive steps of the peak grouping algorithm. peaks are plotted as points showing relative intensity. identified groups are flanked by dotted vertical lines">
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	91 <validator type="in_range" message="Must be more than 0" min="0.001" max="inf"/>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	92 </param>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	93 -->
2a104ea58d12 Uploaded lecorguille parents: diff changeset	94
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	95 <expand macro="input_peaklist"/>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	96 </inputs>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	97
2a104ea58d12 Uploaded lecorguille parents: diff changeset	98 <outputs>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	99 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	100 <data name="rplotsPdf" format="pdf" from_work_dir="Rplots.pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
24 1a7d1f9e8912 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b8ea02b3d37550c33dcf8e099fe8c636287b0865 lecorguille parents: 22 diff changeset	101 <expand macro="output_peaklist" function="group"/>
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	102 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	103 </outputs>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	104
2a104ea58d12 Uploaded lecorguille parents: diff changeset	105 <tests>
7 75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	106 <!--<test>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	107 <param name="image" value="xset.RData"/>
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	108 <param name="methods\|method" value="density"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	109 <param name="methods\|bw" value="5"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	110 <param name="methods\|minfrac" value="0.3"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	111 <param name="methods\|mzwid" value="0.01"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	112 <param name="methods\|density_options\|option" value="show"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	113 <param name="methods\|density_options\|max" value="50"/>
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	114 <output name="log">
df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	115 <assert_contents>
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	116 <has_text text="object with 4 samples" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	117 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	118 <has_text text="Mass range: 50.0021-999.9863 m/z" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	119 <has_text text="Peaks: 59359 (about 14840 per sample)" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	120 <has_text text="Peak Groups: 48998" />
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	121 <has_text text="Sample classes: bio, blank" />
df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	122 </assert_contents>
df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	123 </output>
7 75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	124 </test>-->
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	125 <test>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	126 <param name="image" value="faahKO.xset.RData"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	127 <param name="methods\|method" value="density"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	128 <param name="methods\|bw" value="5"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	129 <param name="methods\|minfrac" value="0.3"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	130 <param name="methods\|mzwid" value="0.01"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	131 <param name="methods\|density_options\|option" value="show"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	132 <param name="methods\|density_options\|max" value="50"/>
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	133 <conditional name="peaklist">
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	134 <param name="convertRTMinute" value="false" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	135 <param name="peaklistBool" value="true" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	136 <param name="numDigitsMZ" value="4" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	137 <param name="numDigitsRT" value="1" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	138 </conditional>
7 75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	139 <output name="log">
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	140 <assert_contents>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	141 <has_text text="object with 4 samples" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	142 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	143 <has_text text="Mass range: 200.1-600 m/z" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	144 <has_text text="Peaks: 9251 (about 2313 per sample)" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	145 <has_text text="Peak Groups: 8275" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	146 <has_text text="Sample classes: KO, WT" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	147 </assert_contents>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	148 </output>
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	149 <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	150 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	151 </test>
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	152 <test>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	153 <param name="image" value="faahKO-single-class.xset.merged.RData"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	154 <param name="methods\|method" value="density"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	155 <param name="methods\|bw" value="5"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	156 <param name="methods\|minfrac" value="0.3"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	157 <param name="methods\|mzwid" value="0.01"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	158 <param name="methods\|density_options\|option" value="show"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	159 <param name="methods\|density_options\|max" value="50"/>
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	160 <conditional name="peaklist">
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	161 <param name="convertRTMinute" value="false" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	162 <param name="peaklistBool" value="true" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	163 <param name="numDigitsMZ" value="4" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	164 <param name="numDigitsRT" value="1" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	165 </conditional>
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	166 <output name="log">
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	167 <assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	168 <has_text text="object with 4 samples" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	169 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	170 <has_text text="Mass range: 200.1-600 m/z" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	171 <has_text text="Peaks: 9251 (about 2313 per sample)" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	172 <has_text text="Peak Groups: 8275" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	173 <has_text text="Sample classes: KO, WT" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	174 </assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	175 </output>
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	176 <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	177 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	178 </test>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	179 <test>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	180 <param name="image" value="faahKO-single.xset.merged.RData"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	181 <param name="methods\|method" value="density"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	182 <param name="methods\|bw" value="5"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	183 <param name="methods\|minfrac" value="0.3"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	184 <param name="methods\|mzwid" value="0.01"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	185 <param name="methods\|density_options\|option" value="show"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	186 <param name="methods\|density_options\|max" value="50"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	187 <output name="log">
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	188 <assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	189 <has_text text="object with 4 samples" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	190 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	191 <has_text text="Mass range: 200.1-600 m/z" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	192 <has_text text="Peaks: 9251 (about 2313 per sample)" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	193 <has_text text="Peak Groups: 664" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	194 <has_text text="Sample classes: ." />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	195 </assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	196 </output>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	197 </test>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	198 <test>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	199 <param name="image" value="MM-single.xset.merged.RData"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	200 <param name="methods\|method" value="density"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	201 <param name="methods\|bw" value="5"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	202 <param name="methods\|minfrac" value="0.3"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	203 <param name="methods\|mzwid" value="0.01"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	204 <param name="methods\|density_options\|option" value="show"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	205 <param name="methods\|density_options\|max" value="50"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	206 <output name="log">
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	207 <assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	208 <has_text text="object with 2 samples" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	209 <has_text text="Time range: 19.7-307.3 seconds (0.3-5.1 minutes)" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	210 <has_text text="Mass range: 117.0357-936.7059 m/z" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	211 <has_text text="Peaks: 236 (about 118 per sample)" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	212 <has_text text="Peak Groups: 236" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	213 <has_text text="Sample classes: ." />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	214 </assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	215 </output>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	216 </test>
7 75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	217 <!--<test>
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	218 <param name="image" value="xset.group.retcor.RData"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	219 <param name="methods\|method" value="density"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	220 <param name="methods\|bw" value="5"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	221 <param name="methods\|minfrac" value="0.3"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	222 <param name="methods\|mzwid" value="0.01"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	223 <param name="methods\|density_options\|option" value="show"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	224 <param name="methods\|density_options\|max" value="50"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	225 <output name="log">
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	226 <assert_contents>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	227 <has_text text="object with 4 samples" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	228 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	229 <has_text text="Mass range: 50.0021-999.9863 m/z" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	230 <has_text text="Peaks: 59359 (about 14840 per sample)" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	231 <has_text text="Peak Groups: 48958" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	232 <has_text text="Sample classes: bio, blank" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	233 </assert_contents>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	234 </output>
7 75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	235 </test>-->
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	236 <test>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	237 <param name="image" value="faahKO.xset.group.retcor.RData"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	238 <param name="methods\|method" value="density"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	239 <param name="methods\|bw" value="5"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	240 <param name="methods\|minfrac" value="0.3"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	241 <param name="methods\|mzwid" value="0.01"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	242 <param name="methods\|density_options\|option" value="show"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	243 <param name="methods\|density_options\|max" value="50"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	244 <output name="log">
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	245 <assert_contents>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	246 <has_text text="object with 4 samples" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	247 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	248 <has_text text="Mass range: 200.1-600 m/z" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	249 <has_text text="Peaks: 9251 (about 2313 per sample)" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	250 <has_text text="Peak Groups: 8157" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	251 <has_text text="Sample classes: KO, WT" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	252 </assert_contents>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	253 </output>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	254 </test>
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	255 <test>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	256 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	257 <param name="methods\|method" value="density"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	258 <param name="methods\|bw" value="5"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	259 <param name="methods\|minfrac" value="0.3"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	260 <param name="methods\|mzwid" value="0.01"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	261 <param name="methods\|density_options\|option" value="show"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	262 <param name="methods\|density_options\|max" value="50"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	263 <output name="log">
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	264 <assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	265 <has_text text="object with 4 samples" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	266 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	267 <has_text text="Mass range: 200.1-600 m/z" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	268 <has_text text="Peaks: 9251 (about 2313 per sample)" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	269 <has_text text="Peak Groups: 8157" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	270 <has_text text="Sample classes: KO, WT" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	271 </assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	272 </output>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	273 </test>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	274 </tests>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	275
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	276 <help><![CDATA[
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	277
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	278 @HELP_AUTHORS@
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	279
2a104ea58d12 Uploaded lecorguille parents: diff changeset	280 ==========
2a104ea58d12 Uploaded lecorguille parents: diff changeset	281 Xcms.Group
2a104ea58d12 Uploaded lecorguille parents: diff changeset	282 ==========
2a104ea58d12 Uploaded lecorguille parents: diff changeset	283
2a104ea58d12 Uploaded lecorguille parents: diff changeset	284 Description
2a104ea58d12 Uploaded lecorguille parents: diff changeset	285 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	286
2a104ea58d12 Uploaded lecorguille parents: diff changeset	287 After peak identification with xcmsSet, this tool groups the peaks which represent the same analyte across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. Allows rejection of features, which are only partially detected within the replicates of a sample class.
2a104ea58d12 Uploaded lecorguille parents: diff changeset	288
2a104ea58d12 Uploaded lecorguille parents: diff changeset	289
2a104ea58d12 Uploaded lecorguille parents: diff changeset	290 Workflow position
2a104ea58d12 Uploaded lecorguille parents: diff changeset	291 -----------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	292
2a104ea58d12 Uploaded lecorguille parents: diff changeset	293 Upstream tools
2a104ea58d12 Uploaded lecorguille parents: diff changeset	294
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	295 +------------------------+-----------------+--------------------+------------+
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	296 \| Name \| output file \| format \| parameter \|
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	297 +========================+=================+====================+============+
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	298 \| xcms.xcmsSet \| xset.RData \| rdata.xcms.raw \| RData file \|
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	299 +------------------------+-----------------+--------------------+------------+
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	300 \| xcms.xcmsSet Merger \| xset.RData \| rdata.xcms.raw \| RData file \|
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	301 +------------------------+-----------------+--------------------+------------+
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	302 \| xcms.retcor \| xset.RData \| rdata.xcms.retcor \| RData file \|
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	303 +------------------------+-----------------+--------------------+------------+
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	304
2a104ea58d12 Uploaded lecorguille parents: diff changeset	305
2a104ea58d12 Uploaded lecorguille parents: diff changeset	306 Downstream tools
2a104ea58d12 Uploaded lecorguille parents: diff changeset	307
2a104ea58d12 Uploaded lecorguille parents: diff changeset	308 +---------------------------+--------------------------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	309 \| Name \| Output file \| Format \|
2a104ea58d12 Uploaded lecorguille parents: diff changeset	310 +===========================+=================+====================+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	311 \|xcms.retcor \| xset.RData \| rdata.xcms.group \|
2a104ea58d12 Uploaded lecorguille parents: diff changeset	312 +---------------------------+--------------------------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	313 \|xcms.fillPeaks \| xset.RData \| rdata.xcms.group \|
2a104ea58d12 Uploaded lecorguille parents: diff changeset	314 +---------------------------+--------------------------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	315
2a104ea58d12 Uploaded lecorguille parents: diff changeset	316 General schema of the metabolomic workflow
2a104ea58d12 Uploaded lecorguille parents: diff changeset	317
2a104ea58d12 Uploaded lecorguille parents: diff changeset	318 .. image:: xcms_group_workflow.png
2a104ea58d12 Uploaded lecorguille parents: diff changeset	319
2a104ea58d12 Uploaded lecorguille parents: diff changeset	320
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	321 ---------------------------------------------------
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	322
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	323 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	324 Input files
2a104ea58d12 Uploaded lecorguille parents: diff changeset	325 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	326
2a104ea58d12 Uploaded lecorguille parents: diff changeset	327 +---------------------------+-----------------------+
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	328 \| Parameter \| Format \|
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	329 +===========================+=======================+
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	330 \| OR : RData file \| rdata.xcms.raw \|
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	331 +---------------------------+-----------------------+
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	332 \| OR : RData file \| rdata.xcms.retcor \|
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	333 +---------------------------+-----------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	334
2a104ea58d12 Uploaded lecorguille parents: diff changeset	335
2a104ea58d12 Uploaded lecorguille parents: diff changeset	336 ----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	337 Parameters
2a104ea58d12 Uploaded lecorguille parents: diff changeset	338 ----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	339
2a104ea58d12 Uploaded lecorguille parents: diff changeset	340 Method to use for grouping
2a104ea58d12 Uploaded lecorguille parents: diff changeset	341 --------------------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	342
2a104ea58d12 Uploaded lecorguille parents: diff changeset	343 mzClust
2a104ea58d12 Uploaded lecorguille parents: diff changeset	344
2a104ea58d12 Uploaded lecorguille parents: diff changeset	345 \| Runs high resolution alignment on single spectra samples stored in the RData file generated by the xcmsSet tool.
2a104ea58d12 Uploaded lecorguille parents: diff changeset	346
2a104ea58d12 Uploaded lecorguille parents: diff changeset	347 density
2a104ea58d12 Uploaded lecorguille parents: diff changeset	348
2a104ea58d12 Uploaded lecorguille parents: diff changeset	349 \| Groups peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.
2a104ea58d12 Uploaded lecorguille parents: diff changeset	350
2a104ea58d12 Uploaded lecorguille parents: diff changeset	351 nearest
2a104ea58d12 Uploaded lecorguille parents: diff changeset	352
2a104ea58d12 Uploaded lecorguille parents: diff changeset	353 \| Groups peaks together across samples by creating a master peak list and assigning corresponding peaks from all samples. It is inspired by the alignment algorithm of mzMine.
2a104ea58d12 Uploaded lecorguille parents: diff changeset	354
2a104ea58d12 Uploaded lecorguille parents: diff changeset	355
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	356 @HELP_GET_PEAK_LIST@
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	357
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	358 ------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	359 Output files
2a104ea58d12 Uploaded lecorguille parents: diff changeset	360 ------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	361
2a104ea58d12 Uploaded lecorguille parents: diff changeset	362 xset.group.RData: rdata.xcms.group format
2a104ea58d12 Uploaded lecorguille parents: diff changeset	363
2a104ea58d12 Uploaded lecorguille parents: diff changeset	364 \| Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks).
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	365
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	366 xset.group.Rplots.pdf
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	367
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	368 @HELP_GET_PEAK_LIST_OUTPUTS@
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	369
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	370
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	371 ---------------------------------------------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	372
2a104ea58d12 Uploaded lecorguille parents: diff changeset	373
2a104ea58d12 Uploaded lecorguille parents: diff changeset	374 ---------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	375 Working example
2a104ea58d12 Uploaded lecorguille parents: diff changeset	376 ---------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	377
2a104ea58d12 Uploaded lecorguille parents: diff changeset	378 Input files
2a104ea58d12 Uploaded lecorguille parents: diff changeset	379 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	380
2a104ea58d12 Uploaded lecorguille parents: diff changeset	381 \| RData file -> xset.RData
2a104ea58d12 Uploaded lecorguille parents: diff changeset	382
2a104ea58d12 Uploaded lecorguille parents: diff changeset	383 Parameters
2a104ea58d12 Uploaded lecorguille parents: diff changeset	384 ----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	385
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	386 \| Method: density
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	387 \| bw: 10
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	388 \| minfrac: 0.5
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	389 \| mzwid: 0.05
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	390 \| Advanced options: show
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	391 \| max: 10
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	392
2a104ea58d12 Uploaded lecorguille parents: diff changeset	393
3 003373d58672 planemo upload lecorguille parents: 2 diff changeset	394 ---------------------------------------------------
003373d58672 planemo upload lecorguille parents: 2 diff changeset	395
003373d58672 planemo upload lecorguille parents: 2 diff changeset	396 Changelog/News
003373d58672 planemo upload lecorguille parents: 2 diff changeset	397 --------------
003373d58672 planemo upload lecorguille parents: 2 diff changeset	398
19 7f667b64d5a5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 17 diff changeset	399 Version 2.1.0 - 07/02/2017
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	400
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	401 - IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	402
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	403 - IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger"
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	404
22 b41669de74ae planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 19 diff changeset	405 - BUGFIX: the default value of "density" -> "Maximum number of groups to identify in a single m/z slice" which was of 5 have been changed to fix with the XMCS default values to 50
b41669de74ae planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 19 diff changeset	406
10 676c748b23ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	407 Version 2.0.6 - 06/07/2016
676c748b23ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	408
676c748b23ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	409 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
676c748b23ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	410
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	411 Version 2.0.5 - 04/04/2016
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	412
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	413 - TEST: refactoring to pass planemo test using conda dependencies
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	414
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	415
3 003373d58672 planemo upload lecorguille parents: 2 diff changeset	416 Version 2.0.4 - 10/02/2016
003373d58672 planemo upload lecorguille parents: 2 diff changeset	417
003373d58672 planemo upload lecorguille parents: 2 diff changeset	418 - BUGFIX: better management of errors. Datasets remained green although the process failed
003373d58672 planemo upload lecorguille parents: 2 diff changeset	419
003373d58672 planemo upload lecorguille parents: 2 diff changeset	420 - UPDATE: refactoring of internal management of inputs/outputs
003373d58672 planemo upload lecorguille parents: 2 diff changeset	421
003373d58672 planemo upload lecorguille parents: 2 diff changeset	422 - UPDATE: refactoring to feed the new report tool
003373d58672 planemo upload lecorguille parents: 2 diff changeset	423
003373d58672 planemo upload lecorguille parents: 2 diff changeset	424
003373d58672 planemo upload lecorguille parents: 2 diff changeset	425 Version 2.0.2 - 02/06/2015
003373d58672 planemo upload lecorguille parents: 2 diff changeset	426
003373d58672 planemo upload lecorguille parents: 2 diff changeset	427 - 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.
003373d58672 planemo upload lecorguille parents: 2 diff changeset	428
003373d58672 planemo upload lecorguille parents: 2 diff changeset	429 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
003373d58672 planemo upload lecorguille parents: 2 diff changeset	430
003373d58672 planemo upload lecorguille parents: 2 diff changeset	431
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	432 ]]></help>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	433
2a104ea58d12 Uploaded lecorguille parents: diff changeset	434
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	435 <expand macro="citation" />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	436
2a104ea58d12 Uploaded lecorguille parents: diff changeset	437
2a104ea58d12 Uploaded lecorguille parents: diff changeset	438 </tool>

Mercurial > repos > lecorguille > xcms_group

annotate abims_xcms_group.xml @ 27:36b470f3ebcf draft