xcms_group: abims_xcms_group.xml annotate

annotate abims_xcms_group.xml @ 26:e121f6d76dfb draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a0206fe6932fda018ecd078134d884aec36aeb97

author	lecorguille
date	Fri, 19 May 2017 09:35:20 -0400
parents	1a7d1f9e8912
children	36b470f3ebcf

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'
7f667b64d5a5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 17 diff changeset	18 rplotspdf '$rplotsPdf'
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	19
26 e121f6d76dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a0206fe6932fda018ecd078134d884aec36aeb97 lecorguille parents: 24 diff changeset	20 method $methods.method
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	21 #if $methods.method == "density":
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	22 ## minsamp $methods.minsamp
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	23 minfrac $methods.minfrac
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	24 bw $methods.bw
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	25 mzwid $methods.mzwid
26 e121f6d76dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a0206fe6932fda018ecd078134d884aec36aeb97 lecorguille parents: 24 diff changeset	26 sleep 0.001
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	27 #if $methods.density_options.option == "show":
2a104ea58d12 Uploaded lecorguille parents: diff changeset	28 max $methods.density_options.max
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	29 #end if
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	30 #elif $methods.method == "mzClust":
2a104ea58d12 Uploaded lecorguille parents: diff changeset	31 mzppm $methods.mzppm
2a104ea58d12 Uploaded lecorguille parents: diff changeset	32 mzabs $methods.mzabs
2a104ea58d12 Uploaded lecorguille parents: diff changeset	33 minfrac $methods.minfrac
2a104ea58d12 Uploaded lecorguille parents: diff changeset	34 ## minsamp $methods.minsamp
2a104ea58d12 Uploaded lecorguille parents: diff changeset	35 #else:
2a104ea58d12 Uploaded lecorguille parents: diff changeset	36 mzVsRTbalance $methods.mzVsRTbalance
2a104ea58d12 Uploaded lecorguille parents: diff changeset	37 mzCheck $methods.mzCheck
2a104ea58d12 Uploaded lecorguille parents: diff changeset	38 rtCheck $methods.rtCheck
2a104ea58d12 Uploaded lecorguille parents: diff changeset	39 kNN $methods.kNN
2a104ea58d12 Uploaded lecorguille parents: diff changeset	40 #end if
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	41
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	42 @COMMAND_PEAKLIST@
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	43
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	44 @COMMAND_LOG_EXIT@
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	45 ]]></command>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	46
2a104ea58d12 Uploaded lecorguille parents: diff changeset	47 <inputs>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	48 <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	49 <conditional name="methods">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	50 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	51 <option value="density" selected="true">density</option>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	52 <option value="mzClust" >mzClust</option>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	53 <option value="nearest" >nearest</option>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	54 </param>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	55 <when value="density">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	56 <param name="bw" type="integer" 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" />
2a104ea58d12 Uploaded lecorguille parents: diff changeset	57 <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	58 <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	59 <!--
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	60 <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	61 -->
2a104ea58d12 Uploaded lecorguille parents: diff changeset	62 <conditional name="density_options">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	63 <param name="option" type="select" label="Advanced options">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	64 <option value="show">show</option>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	65 <option value="hide" selected="true">hide</option>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	66 </param>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	67 <when value="show">
22 b41669de74ae planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 19 diff changeset	68 <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	69 </when>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	70 <when value="hide">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	71 </when>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	72 </conditional>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	73
2a104ea58d12 Uploaded lecorguille parents: diff changeset	74 </when>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	75 <when value="mzClust">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	76 <param name="mzppm" type="integer" value="20 " label="Relative error used for clustering/grouping in ppm" help="[mzppm]" />
2a104ea58d12 Uploaded lecorguille parents: diff changeset	77 <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" />
2a104ea58d12 Uploaded lecorguille parents: diff changeset	78 <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	79 <!--
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	80 <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	81 -->
2a104ea58d12 Uploaded lecorguille parents: diff changeset	82 </when>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	83 <when value="nearest">
2a104ea58d12 Uploaded lecorguille parents: diff changeset	84 <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	85 <param name="mzCheck" type="float" value="0.2" label="Maximum tolerated distance for mz" help="[mzCheck]" />
2a104ea58d12 Uploaded lecorguille parents: diff changeset	86 <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	87 <param name="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" help="[kNN]" />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	88 </when>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	89 </conditional>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	90 <!--
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	91 <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	92 <validator type="in_range" message="Must be more than 0" min="0.001" max="inf"/>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	93 </param>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	94 -->
2a104ea58d12 Uploaded lecorguille parents: diff changeset	95
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	96 <expand macro="input_peaklist"/>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	97 </inputs>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	98
2a104ea58d12 Uploaded lecorguille parents: diff changeset	99 <outputs>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	100 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	101 <data name="rplotsPdf" format="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	102 <expand macro="output_peaklist" function="group"/>
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	103 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	104 </outputs>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	105
2a104ea58d12 Uploaded lecorguille parents: diff changeset	106 <tests>
7 75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	107 <!--<test>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	108 <param name="image" value="xset.RData"/>
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	109 <param name="methods\|method" value="density"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	110 <param name="methods\|bw" value="5"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	111 <param name="methods\|minfrac" value="0.3"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	112 <param name="methods\|mzwid" value="0.01"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	113 <param name="methods\|density_options\|option" value="show"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	114 <param name="methods\|density_options\|max" value="50"/>
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	115 <output name="log">
df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	116 <assert_contents>
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	117 <has_text text="object with 4 samples" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	118 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	119 <has_text text="Mass range: 50.0021-999.9863 m/z" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	120 <has_text text="Peaks: 59359 (about 14840 per sample)" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	121 <has_text text="Peak Groups: 48998" />
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	122 <has_text text="Sample classes: bio, blank" />
df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	123 </assert_contents>
df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	124 </output>
7 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 <test>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	127 <param name="image" value="faahKO.xset.RData"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	128 <param name="methods\|method" value="density"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	129 <param name="methods\|bw" value="5"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	130 <param name="methods\|minfrac" value="0.3"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	131 <param name="methods\|mzwid" value="0.01"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	132 <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	133 <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	134 <conditional name="peaklist">
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	135 <param name="convertRTMinute" value="false" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	136 <param name="peaklistBool" value="true" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	137 <param name="numDigitsMZ" value="4" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	138 <param name="numDigitsRT" value="1" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	139 </conditional>
7 75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	140 <output name="log">
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	141 <assert_contents>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	142 <has_text text="object with 4 samples" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	143 <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	144 <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	145 <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	146 <has_text text="Peak Groups: 8275" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	147 <has_text text="Sample classes: KO, WT" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	148 </assert_contents>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	149 </output>
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	150 <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	151 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	152 </test>
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	153 <test>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	154 <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	155 <param name="methods\|method" value="density"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	156 <param name="methods\|bw" value="5"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	157 <param name="methods\|minfrac" value="0.3"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	158 <param name="methods\|mzwid" value="0.01"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	159 <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	160 <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	161 <conditional name="peaklist">
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	162 <param name="convertRTMinute" value="false" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	163 <param name="peaklistBool" value="true" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	164 <param name="numDigitsMZ" value="4" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	165 <param name="numDigitsRT" value="1" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	166 </conditional>
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	167 <output name="log">
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	168 <assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	169 <has_text text="object with 4 samples" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	170 <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	171 <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	172 <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	173 <has_text text="Peak Groups: 8275" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	174 <has_text text="Sample classes: KO, WT" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	175 </assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	176 </output>
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	177 <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	178 <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	179 </test>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	180 <test>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	181 <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	182 <param name="methods\|method" value="density"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	183 <param name="methods\|bw" value="5"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	184 <param name="methods\|minfrac" value="0.3"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	185 <param name="methods\|mzwid" value="0.01"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	186 <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	187 <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	188 <output name="log">
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	189 <assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	190 <has_text text="object with 4 samples" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	191 <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	192 <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	193 <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	194 <has_text text="Peak Groups: 664" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	195 <has_text text="Sample classes: ." />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	196 </assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	197 </output>
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 <test>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	200 <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	201 <param name="methods\|method" value="density"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	202 <param name="methods\|bw" value="5"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	203 <param name="methods\|minfrac" value="0.3"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	204 <param name="methods\|mzwid" value="0.01"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	205 <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	206 <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	207 <output name="log">
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	208 <assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	209 <has_text text="object with 2 samples" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	210 <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	211 <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	212 <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	213 <has_text text="Peak Groups: 236" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	214 <has_text text="Sample classes: ." />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	215 </assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	216 </output>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	217 </test>
7 75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	218 <!--<test>
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	219 <param name="image" value="xset.group.retcor.RData"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	220 <param name="methods\|method" value="density"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	221 <param name="methods\|bw" value="5"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	222 <param name="methods\|minfrac" value="0.3"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	223 <param name="methods\|mzwid" value="0.01"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	224 <param name="methods\|density_options\|option" value="show"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	225 <param name="methods\|density_options\|max" value="50"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	226 <output name="log">
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	227 <assert_contents>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	228 <has_text text="object with 4 samples" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	229 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	230 <has_text text="Mass range: 50.0021-999.9863 m/z" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	231 <has_text text="Peaks: 59359 (about 14840 per sample)" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	232 <has_text text="Peak Groups: 48958" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	233 <has_text text="Sample classes: bio, blank" />
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	234 </assert_contents>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	235 </output>
7 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 <test>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	238 <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	239 <param name="methods\|method" value="density"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	240 <param name="methods\|bw" value="5"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	241 <param name="methods\|minfrac" value="0.3"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	242 <param name="methods\|mzwid" value="0.01"/>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	243 <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	244 <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	245 <output name="log">
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	246 <assert_contents>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	247 <has_text text="object with 4 samples" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	248 <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	249 <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	250 <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	251 <has_text text="Peak Groups: 8157" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	252 <has_text text="Sample classes: KO, WT" />
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	253 </assert_contents>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	254 </output>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	255 </test>
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	256 <test>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	257 <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	258 <param name="methods\|method" value="density"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	259 <param name="methods\|bw" value="5"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	260 <param name="methods\|minfrac" value="0.3"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	261 <param name="methods\|mzwid" value="0.01"/>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	262 <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	263 <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	264 <output name="log">
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	265 <assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	266 <has_text text="object with 4 samples" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	267 <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	268 <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	269 <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	270 <has_text text="Peak Groups: 8157" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	271 <has_text text="Sample classes: KO, WT" />
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	272 </assert_contents>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	273 </output>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	274 </test>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	275 </tests>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	276
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	277 <help><![CDATA[
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	278
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	279 @HELP_AUTHORS@
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	280
2a104ea58d12 Uploaded lecorguille parents: diff changeset	281 ==========
2a104ea58d12 Uploaded lecorguille parents: diff changeset	282 Xcms.Group
2a104ea58d12 Uploaded lecorguille parents: diff changeset	283 ==========
2a104ea58d12 Uploaded lecorguille parents: diff changeset	284
2a104ea58d12 Uploaded lecorguille parents: diff changeset	285 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	286 Description
2a104ea58d12 Uploaded lecorguille parents: diff changeset	287 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	288
2a104ea58d12 Uploaded lecorguille parents: diff changeset	289 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	290
2a104ea58d12 Uploaded lecorguille parents: diff changeset	291
2a104ea58d12 Uploaded lecorguille parents: diff changeset	292
2a104ea58d12 Uploaded lecorguille parents: diff changeset	293 -----------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	294 Workflow position
2a104ea58d12 Uploaded lecorguille parents: diff changeset	295 -----------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	296
2a104ea58d12 Uploaded lecorguille parents: diff changeset	297 Upstream tools
2a104ea58d12 Uploaded lecorguille parents: diff changeset	298
2a104ea58d12 Uploaded lecorguille parents: diff changeset	299 ========================= ================= =================== ==========
2a104ea58d12 Uploaded lecorguille parents: diff changeset	300 Name output file format parameter
2a104ea58d12 Uploaded lecorguille parents: diff changeset	301 ========================= ================= =================== ==========
2a104ea58d12 Uploaded lecorguille parents: diff changeset	302 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
2a104ea58d12 Uploaded lecorguille parents: diff changeset	303 ------------------------- ----------------- ------------------- ----------
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	304 xcms.xcmsSet Merger xset.RData rdata.xcms.raw RData file
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	305 ------------------------- ----------------- ------------------- ----------
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	306 xcms.retcor xset.RData rdata.xcms.retcor RData file
2a104ea58d12 Uploaded lecorguille parents: diff changeset	307 ========================= ================= =================== ==========
2a104ea58d12 Uploaded lecorguille parents: diff changeset	308
2a104ea58d12 Uploaded lecorguille parents: diff changeset	309
2a104ea58d12 Uploaded lecorguille parents: diff changeset	310 Downstream tools
2a104ea58d12 Uploaded lecorguille parents: diff changeset	311
2a104ea58d12 Uploaded lecorguille parents: diff changeset	312 +---------------------------+--------------------------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	313 \| Name \| Output file \| Format \|
2a104ea58d12 Uploaded lecorguille parents: diff changeset	314 +===========================+=================+====================+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	315 \|xcms.retcor \| xset.RData \| rdata.xcms.group \|
2a104ea58d12 Uploaded lecorguille parents: diff changeset	316 +---------------------------+--------------------------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	317 \|xcms.fillPeaks \| xset.RData \| rdata.xcms.group \|
2a104ea58d12 Uploaded lecorguille parents: diff changeset	318 +---------------------------+--------------------------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	319
2a104ea58d12 Uploaded lecorguille parents: diff changeset	320 The output file is an xcmsSet.RData file. You can continue your analysis using it in xcms.retcor tool as an next step and then xcms.fillPeaks.
2a104ea58d12 Uploaded lecorguille parents: diff changeset	321
2a104ea58d12 Uploaded lecorguille parents: diff changeset	322 General schema of the metabolomic workflow
2a104ea58d12 Uploaded lecorguille parents: diff changeset	323
2a104ea58d12 Uploaded lecorguille parents: diff changeset	324 .. image:: xcms_group_workflow.png
2a104ea58d12 Uploaded lecorguille parents: diff changeset	325
2a104ea58d12 Uploaded lecorguille parents: diff changeset	326
2a104ea58d12 Uploaded lecorguille parents: diff changeset	327 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	328 Input files
2a104ea58d12 Uploaded lecorguille parents: diff changeset	329 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	330
2a104ea58d12 Uploaded lecorguille parents: diff changeset	331 +---------------------------+-----------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	332 \| Parameter : num + label \| Format \|
2a104ea58d12 Uploaded lecorguille parents: diff changeset	333 +===========================+=======================+
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	334 \| Or : RData file \| rdata.xcms.raw \|
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	335 +---------------------------+-----------------------+
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	336 \| Or : RData file \| rdata.xcms.retcor \|
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	337 +---------------------------+-----------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	338
2a104ea58d12 Uploaded lecorguille parents: diff changeset	339
2a104ea58d12 Uploaded lecorguille parents: diff changeset	340 ----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	341 Parameters
2a104ea58d12 Uploaded lecorguille parents: diff changeset	342 ----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	343
2a104ea58d12 Uploaded lecorguille parents: diff changeset	344 Method to use for grouping
2a104ea58d12 Uploaded lecorguille parents: diff changeset	345 --------------------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	346
2a104ea58d12 Uploaded lecorguille parents: diff changeset	347 mzClust
2a104ea58d12 Uploaded lecorguille parents: diff changeset	348
2a104ea58d12 Uploaded lecorguille parents: diff changeset	349 \| Runs high resolution alignment on single spectra samples stored in the RData file generated by the xcmsSet tool.
2a104ea58d12 Uploaded lecorguille parents: diff changeset	350
2a104ea58d12 Uploaded lecorguille parents: diff changeset	351 density
2a104ea58d12 Uploaded lecorguille parents: diff changeset	352
2a104ea58d12 Uploaded lecorguille parents: diff changeset	353 \| 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	354
2a104ea58d12 Uploaded lecorguille parents: diff changeset	355 nearest
2a104ea58d12 Uploaded lecorguille parents: diff changeset	356
2a104ea58d12 Uploaded lecorguille parents: diff changeset	357 \| 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	358
2a104ea58d12 Uploaded lecorguille parents: diff changeset	359
2a104ea58d12 Uploaded lecorguille parents: diff changeset	360 ------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	361 Output files
2a104ea58d12 Uploaded lecorguille parents: diff changeset	362 ------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	363
2a104ea58d12 Uploaded lecorguille parents: diff changeset	364 xset.group.Rplots.pdf
2a104ea58d12 Uploaded lecorguille parents: diff changeset	365
2a104ea58d12 Uploaded lecorguille parents: diff changeset	366 xset.group.RData: rdata.xcms.group format
2a104ea58d12 Uploaded lecorguille parents: diff changeset	367
2a104ea58d12 Uploaded lecorguille parents: diff changeset	368 \| 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	369
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	370
2a104ea58d12 Uploaded lecorguille parents: diff changeset	371 ------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	372
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	373 .. class:: infomark
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	374
2a104ea58d12 Uploaded lecorguille parents: diff changeset	375 The output file is an xset.group.RData file. You can continue your analysis using it in xcms.retcor tool.
2a104ea58d12 Uploaded lecorguille parents: diff changeset	376
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	377
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	378 ---------------------------------------------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	379
2a104ea58d12 Uploaded lecorguille parents: diff changeset	380
2a104ea58d12 Uploaded lecorguille parents: diff changeset	381 ---------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	382 Working example
2a104ea58d12 Uploaded lecorguille parents: diff changeset	383 ---------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	384
2a104ea58d12 Uploaded lecorguille parents: diff changeset	385 Input files
2a104ea58d12 Uploaded lecorguille parents: diff changeset	386 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	387
2a104ea58d12 Uploaded lecorguille parents: diff changeset	388 \| RData file -> xset.RData
2a104ea58d12 Uploaded lecorguille parents: diff changeset	389
2a104ea58d12 Uploaded lecorguille parents: diff changeset	390 Parameters
2a104ea58d12 Uploaded lecorguille parents: diff changeset	391 ----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	392
2a104ea58d12 Uploaded lecorguille parents: diff changeset	393 \| Method -> density
2a104ea58d12 Uploaded lecorguille parents: diff changeset	394 \| bw -> 5
2a104ea58d12 Uploaded lecorguille parents: diff changeset	395 \| minfrac -> 0.3
2a104ea58d12 Uploaded lecorguille parents: diff changeset	396 \| mzwid -> 0.01
2a104ea58d12 Uploaded lecorguille parents: diff changeset	397 \| Advanced options: show
2a104ea58d12 Uploaded lecorguille parents: diff changeset	398 \| max -> 50
2a104ea58d12 Uploaded lecorguille parents: diff changeset	399
2a104ea58d12 Uploaded lecorguille parents: diff changeset	400
2a104ea58d12 Uploaded lecorguille parents: diff changeset	401 Output files
2a104ea58d12 Uploaded lecorguille parents: diff changeset	402 ------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	403
2a104ea58d12 Uploaded lecorguille parents: diff changeset	404 \| 1) xset.RData: RData file
2a104ea58d12 Uploaded lecorguille parents: diff changeset	405
2a104ea58d12 Uploaded lecorguille parents: diff changeset	406 \| 2) Example of an xset.group.Rplots pdf file
2a104ea58d12 Uploaded lecorguille parents: diff changeset	407
2a104ea58d12 Uploaded lecorguille parents: diff changeset	408 .. image:: xcms_group.png
2a104ea58d12 Uploaded lecorguille parents: diff changeset	409 :width: 700
2a104ea58d12 Uploaded lecorguille parents: diff changeset	410
2a104ea58d12 Uploaded lecorguille parents: diff changeset	411
3 003373d58672 planemo upload lecorguille parents: 2 diff changeset	412 ---------------------------------------------------
003373d58672 planemo upload lecorguille parents: 2 diff changeset	413
003373d58672 planemo upload lecorguille parents: 2 diff changeset	414 Changelog/News
003373d58672 planemo upload lecorguille parents: 2 diff changeset	415 --------------
003373d58672 planemo upload lecorguille parents: 2 diff changeset	416
19 7f667b64d5a5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 17 diff changeset	417 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	418
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	419 - 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	420
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	421 - 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	422
22 b41669de74ae planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 19 diff changeset	423 - 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	424
10 676c748b23ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	425 Version 2.0.6 - 06/07/2016
676c748b23ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	426
676c748b23ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	427 - 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	428
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	429 Version 2.0.5 - 04/04/2016
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	430
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	431 - TEST: refactoring to pass planemo test using conda dependencies
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	432
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	433
3 003373d58672 planemo upload lecorguille parents: 2 diff changeset	434 Version 2.0.4 - 10/02/2016
003373d58672 planemo upload lecorguille parents: 2 diff changeset	435
003373d58672 planemo upload lecorguille parents: 2 diff changeset	436 - BUGFIX: better management of errors. Datasets remained green although the process failed
003373d58672 planemo upload lecorguille parents: 2 diff changeset	437
003373d58672 planemo upload lecorguille parents: 2 diff changeset	438 - UPDATE: refactoring of internal management of inputs/outputs
003373d58672 planemo upload lecorguille parents: 2 diff changeset	439
003373d58672 planemo upload lecorguille parents: 2 diff changeset	440 - UPDATE: refactoring to feed the new report tool
003373d58672 planemo upload lecorguille parents: 2 diff changeset	441
003373d58672 planemo upload lecorguille parents: 2 diff changeset	442
003373d58672 planemo upload lecorguille parents: 2 diff changeset	443 Version 2.0.2 - 02/06/2015
003373d58672 planemo upload lecorguille parents: 2 diff changeset	444
003373d58672 planemo upload lecorguille parents: 2 diff changeset	445 - 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	446
003373d58672 planemo upload lecorguille parents: 2 diff changeset	447 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
003373d58672 planemo upload lecorguille parents: 2 diff changeset	448
003373d58672 planemo upload lecorguille parents: 2 diff changeset	449
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	450 ]]></help>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	451
2a104ea58d12 Uploaded lecorguille parents: diff changeset	452
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	453 <expand macro="citation" />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	454
2a104ea58d12 Uploaded lecorguille parents: diff changeset	455
2a104ea58d12 Uploaded lecorguille parents: diff changeset	456 </tool>

Mercurial > repos > lecorguille > xcms_group

annotate abims_xcms_group.xml @ 26:e121f6d76dfb draft