xcms_group: abims_xcms_group.xml annotate

annotate abims_xcms_group.xml @ 13:13558e8a4778 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1

author	lecorguille
date	Wed, 29 Nov 2017 09:46:03 -0500
parents	4c8507667cd6
children	833d2c821d9c

rev	line source
13 13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	1 <tool id="abims_xcms_group" name="xcms.group" version="2.1.1">
0 f3f97841564f Uploaded lecorguille parents: diff changeset	2
f3f97841564f 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>
f3f97841564f Uploaded lecorguille parents: diff changeset	4
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	5 <macros>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	6 <import>macros.xml</import>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	7 </macros>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	8
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	9 <expand macro="requirements"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	10 <expand macro="stdio"/>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	11
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	12 <command><![CDATA[
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	13 @COMMAND_XCMS_SCRIPT@
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	14 xfunction group
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	15 image '$image'
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	16
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	17 xsetRdataOutput '$xsetRData'
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	18 rplotspdf '$rplotsPdf'
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	19
13 13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	20 method $methods.method
0 f3f97841564f Uploaded lecorguille parents: diff changeset	21 #if $methods.method == "density":
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	22 ## minsamp $methods.minsamp
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	23 minfrac $methods.minfrac
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	24 bw $methods.bw
0 f3f97841564f Uploaded lecorguille parents: diff changeset	25 mzwid $methods.mzwid
11 9e45e1c404a4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit c12284c89d941da18f30b2666a64434ce1073cea lecorguille parents: 10 diff changeset	26 sleep 0.001
0 f3f97841564f Uploaded lecorguille parents: diff changeset	27 #if $methods.density_options.option == "show":
f3f97841564f Uploaded lecorguille parents: diff changeset	28 max $methods.density_options.max
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	29 #end if
0 f3f97841564f Uploaded lecorguille parents: diff changeset	30 #elif $methods.method == "mzClust":
f3f97841564f Uploaded lecorguille parents: diff changeset	31 mzppm $methods.mzppm
f3f97841564f Uploaded lecorguille parents: diff changeset	32 mzabs $methods.mzabs
f3f97841564f Uploaded lecorguille parents: diff changeset	33 minfrac $methods.minfrac
f3f97841564f Uploaded lecorguille parents: diff changeset	34 ## minsamp $methods.minsamp
f3f97841564f Uploaded lecorguille parents: diff changeset	35 #else:
f3f97841564f Uploaded lecorguille parents: diff changeset	36 mzVsRTbalance $methods.mzVsRTbalance
f3f97841564f Uploaded lecorguille parents: diff changeset	37 mzCheck $methods.mzCheck
f3f97841564f Uploaded lecorguille parents: diff changeset	38 rtCheck $methods.rtCheck
f3f97841564f Uploaded lecorguille parents: diff changeset	39 kNN $methods.kNN
f3f97841564f Uploaded lecorguille parents: diff changeset	40 #end if
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	41
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	42 @COMMAND_PEAKLIST@
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	43
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	44 @COMMAND_LOG_EXIT@
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	45 ]]></command>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	46
f3f97841564f Uploaded lecorguille parents: diff changeset	47 <inputs>
f3f97841564f 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.)" />
f3f97841564f Uploaded lecorguille parents: diff changeset	49 <conditional name="methods">
f3f97841564f Uploaded lecorguille parents: diff changeset	50 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below">
f3f97841564f Uploaded lecorguille parents: diff changeset	51 <option value="density" selected="true">density</option>
f3f97841564f Uploaded lecorguille parents: diff changeset	52 <option value="mzClust" >mzClust</option>
f3f97841564f Uploaded lecorguille parents: diff changeset	53 <option value="nearest" >nearest</option>
f3f97841564f Uploaded lecorguille parents: diff changeset	54 </param>
f3f97841564f Uploaded lecorguille parents: diff changeset	55 <when value="density">
12 4c8507667cd6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e351a27de90aaea30ec193b9663db895bcc7d7d2 lecorguille parents: 11 diff changeset	56 <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 f3f97841564f 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" />
f3f97841564f 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 " />
f3f97841564f Uploaded lecorguille parents: diff changeset	59 <!--
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 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 f3f97841564f Uploaded lecorguille parents: diff changeset	61 -->
f3f97841564f Uploaded lecorguille parents: diff changeset	62 <conditional name="density_options">
f3f97841564f Uploaded lecorguille parents: diff changeset	63 <param name="option" type="select" label="Advanced options">
f3f97841564f Uploaded lecorguille parents: diff changeset	64 <option value="show">show</option>
f3f97841564f Uploaded lecorguille parents: diff changeset	65 <option value="hide" selected="true">hide</option>
f3f97841564f Uploaded lecorguille parents: diff changeset	66 </param>
f3f97841564f Uploaded lecorguille parents: diff changeset	67 <when value="show">
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 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 f3f97841564f Uploaded lecorguille parents: diff changeset	69 </when>
f3f97841564f Uploaded lecorguille parents: diff changeset	70 <when value="hide">
f3f97841564f Uploaded lecorguille parents: diff changeset	71 </when>
f3f97841564f Uploaded lecorguille parents: diff changeset	72 </conditional>
f3f97841564f Uploaded lecorguille parents: diff changeset	73
f3f97841564f Uploaded lecorguille parents: diff changeset	74 </when>
f3f97841564f Uploaded lecorguille parents: diff changeset	75 <when value="mzClust">
f3f97841564f Uploaded lecorguille parents: diff changeset	76 <param name="mzppm" type="integer" value="20 " label="Relative error used for clustering/grouping in ppm" help="[mzppm]" />
f3f97841564f Uploaded lecorguille parents: diff changeset	77 <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" />
f3f97841564f 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" />
f3f97841564f Uploaded lecorguille parents: diff changeset	79 <!--
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 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 f3f97841564f Uploaded lecorguille parents: diff changeset	81 -->
f3f97841564f Uploaded lecorguille parents: diff changeset	82 </when>
f3f97841564f Uploaded lecorguille parents: diff changeset	83 <when value="nearest">
f3f97841564f 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]" />
f3f97841564f Uploaded lecorguille parents: diff changeset	85 <param name="mzCheck" type="float" value="0.2" label="Maximum tolerated distance for mz" help="[mzCheck]" />
f3f97841564f Uploaded lecorguille parents: diff changeset	86 <param name="rtCheck" type="integer" value="15" label="Maximum tolerated distance for RT" help="[rtCheck]" />
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	87 <param name="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" help="[kNN]" />
0 f3f97841564f Uploaded lecorguille parents: diff changeset	88 </when>
f3f97841564f Uploaded lecorguille parents: diff changeset	89 </conditional>
f3f97841564f Uploaded lecorguille parents: diff changeset	90 <!--
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 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 f3f97841564f Uploaded lecorguille parents: diff changeset	92 <validator type="in_range" message="Must be more than 0" min="0.001" max="inf"/>
f3f97841564f Uploaded lecorguille parents: diff changeset	93 </param>
f3f97841564f Uploaded lecorguille parents: diff changeset	94 -->
f3f97841564f Uploaded lecorguille parents: diff changeset	95
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	96 <expand macro="input_peaklist"/>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	97 </inputs>
f3f97841564f Uploaded lecorguille parents: diff changeset	98
f3f97841564f Uploaded lecorguille parents: diff changeset	99 <outputs>
f3f97841564f Uploaded lecorguille parents: diff changeset	100 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
f3f97841564f Uploaded lecorguille parents: diff changeset	101 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	102 <expand macro="output_peaklist" function="group"/>
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	103 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
0 f3f97841564f Uploaded lecorguille parents: diff changeset	104 </outputs>
f3f97841564f Uploaded lecorguille parents: diff changeset	105
f3f97841564f Uploaded lecorguille parents: diff changeset	106 <tests>
5 0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	107 <!--<test>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	108 <param name="image" value="xset.RData"/>
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	109 <param name="methods\|method" value="density"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	110 <param name="methods\|bw" value="5"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	111 <param name="methods\|minfrac" value="0.3"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	112 <param name="methods\|mzwid" value="0.01"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	113 <param name="methods\|density_options\|option" value="show"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	114 <param name="methods\|density_options\|max" value="50"/>
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	115 <output name="log">
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	116 <assert_contents>
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	117 <has_text text="object with 4 samples" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	118 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	119 <has_text text="Mass range: 50.0021-999.9863 m/z" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	120 <has_text text="Peaks: 59359 (about 14840 per sample)" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	121 <has_text text="Peak Groups: 48998" />
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	122 <has_text text="Sample classes: bio, blank" />
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	123 </assert_contents>
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	124 </output>
5 0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	125 </test>-->
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	126 <test>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	127 <param name="image" value="faahKO.xset.RData"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	128 <param name="methods\|method" value="density"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	129 <param name="methods\|bw" value="5"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	130 <param name="methods\|minfrac" value="0.3"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	131 <param name="methods\|mzwid" value="0.01"/>
0306a96cc446 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"/>
0306a96cc446 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"/>
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	134 <conditional name="peaklist">
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	135 <param name="convertRTMinute" value="false" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	136 <param name="peaklistBool" value="true" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	137 <param name="numDigitsMZ" value="4" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	138 <param name="numDigitsRT" value="1" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	139 </conditional>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	140 <output name="log">
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	141 <assert_contents>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	142 <has_text text="object with 4 samples" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	143 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	144 <has_text text="Mass range: 200.1-600 m/z" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	145 <has_text text="Peaks: 9251 (about 2313 per sample)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	146 <has_text text="Peak Groups: 8275" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	147 <has_text text="Sample classes: KO, WT" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	148 </assert_contents>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	149 </output>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	150 <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	151 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	152 </test>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	153 <test>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	154 <param name="image" value="faahKO-single-class.xset.merged.RData"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	155 <param name="methods\|method" value="density"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	156 <param name="methods\|bw" value="5"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	157 <param name="methods\|minfrac" value="0.3"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	158 <param name="methods\|mzwid" value="0.01"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	159 <param name="methods\|density_options\|option" value="show"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	160 <param name="methods\|density_options\|max" value="50"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	161 <conditional name="peaklist">
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	162 <param name="convertRTMinute" value="false" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	163 <param name="peaklistBool" value="true" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	164 <param name="numDigitsMZ" value="4" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	165 <param name="numDigitsRT" value="1" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	166 </conditional>
5 0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	167 <output name="log">
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	168 <assert_contents>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	169 <has_text text="object with 4 samples" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	170 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	171 <has_text text="Mass range: 200.1-600 m/z" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	172 <has_text text="Peaks: 9251 (about 2313 per sample)" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	173 <has_text text="Peak Groups: 8275" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	174 <has_text text="Sample classes: KO, WT" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	175 </assert_contents>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	176 </output>
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	177 <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	178 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	179 </test>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	180 <test>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	181 <param name="image" value="faahKO-single.xset.merged.RData"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	182 <param name="methods\|method" value="density"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	183 <param name="methods\|bw" value="5"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	184 <param name="methods\|minfrac" value="0.3"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	185 <param name="methods\|mzwid" value="0.01"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	186 <param name="methods\|density_options\|option" value="show"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	187 <param name="methods\|density_options\|max" value="50"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	188 <output name="log">
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	189 <assert_contents>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	190 <has_text text="object with 4 samples" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	191 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	192 <has_text text="Mass range: 200.1-600 m/z" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	193 <has_text text="Peaks: 9251 (about 2313 per sample)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	194 <has_text text="Peak Groups: 664" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	195 <has_text text="Sample classes: ." />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	196 </assert_contents>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	197 </output>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	198 </test>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	199 <test>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	200 <param name="image" value="MM-single.xset.merged.RData"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	201 <param name="methods\|method" value="density"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	202 <param name="methods\|bw" value="5"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	203 <param name="methods\|minfrac" value="0.3"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	204 <param name="methods\|mzwid" value="0.01"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	205 <param name="methods\|density_options\|option" value="show"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	206 <param name="methods\|density_options\|max" value="50"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	207 <output name="log">
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	208 <assert_contents>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	209 <has_text text="object with 2 samples" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	210 <has_text text="Time range: 19.7-307.3 seconds (0.3-5.1 minutes)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	211 <has_text text="Mass range: 117.0357-936.7059 m/z" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	212 <has_text text="Peaks: 236 (about 118 per sample)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	213 <has_text text="Peak Groups: 236" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	214 <has_text text="Sample classes: ." />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	215 </assert_contents>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	216 </output>
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	217 </test>
5 0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	218 <!--<test>
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	219 <param name="image" value="xset.group.retcor.RData"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	220 <param name="methods\|method" value="density"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	221 <param name="methods\|bw" value="5"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	222 <param name="methods\|minfrac" value="0.3"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	223 <param name="methods\|mzwid" value="0.01"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	224 <param name="methods\|density_options\|option" value="show"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	225 <param name="methods\|density_options\|max" value="50"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	226 <output name="log">
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	227 <assert_contents>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	228 <has_text text="object with 4 samples" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	229 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	230 <has_text text="Mass range: 50.0021-999.9863 m/z" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	231 <has_text text="Peaks: 59359 (about 14840 per sample)" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	232 <has_text text="Peak Groups: 48958" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	233 <has_text text="Sample classes: bio, blank" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	234 </assert_contents>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	235 </output>
5 0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	236 </test>-->
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	237 <test>
0306a96cc446 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"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	239 <param name="methods\|method" value="density"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	240 <param name="methods\|bw" value="5"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	241 <param name="methods\|minfrac" value="0.3"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	242 <param name="methods\|mzwid" value="0.01"/>
0306a96cc446 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"/>
0306a96cc446 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"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	245 <output name="log">
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	246 <assert_contents>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	247 <has_text text="object with 4 samples" />
0306a96cc446 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)" />
0306a96cc446 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" />
0306a96cc446 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)" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	251 <has_text text="Peak Groups: 8157" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	252 <has_text text="Sample classes: KO, WT" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	253 </assert_contents>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	254 </output>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	255 </test>
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	256 <test>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	257 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	258 <param name="methods\|method" value="density"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	259 <param name="methods\|bw" value="5"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	260 <param name="methods\|minfrac" value="0.3"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	261 <param name="methods\|mzwid" value="0.01"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	262 <param name="methods\|density_options\|option" value="show"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	263 <param name="methods\|density_options\|max" value="50"/>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	264 <output name="log">
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	265 <assert_contents>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	266 <has_text text="object with 4 samples" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	267 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	268 <has_text text="Mass range: 200.1-600 m/z" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	269 <has_text text="Peaks: 9251 (about 2313 per sample)" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	270 <has_text text="Peak Groups: 8157" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	271 <has_text text="Sample classes: KO, WT" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	272 </assert_contents>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	273 </output>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	274 </test>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	275 </tests>
f3f97841564f Uploaded lecorguille parents: diff changeset	276
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	277 <help><![CDATA[
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	278
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	279 @HELP_AUTHORS@
0 f3f97841564f Uploaded lecorguille parents: diff changeset	280
f3f97841564f Uploaded lecorguille parents: diff changeset	281 ==========
f3f97841564f Uploaded lecorguille parents: diff changeset	282 Xcms.Group
f3f97841564f Uploaded lecorguille parents: diff changeset	283 ==========
f3f97841564f Uploaded lecorguille parents: diff changeset	284
f3f97841564f Uploaded lecorguille parents: diff changeset	285 -----------
f3f97841564f Uploaded lecorguille parents: diff changeset	286 Description
f3f97841564f Uploaded lecorguille parents: diff changeset	287 -----------
f3f97841564f Uploaded lecorguille parents: diff changeset	288
f3f97841564f 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.
f3f97841564f Uploaded lecorguille parents: diff changeset	290
f3f97841564f Uploaded lecorguille parents: diff changeset	291
f3f97841564f Uploaded lecorguille parents: diff changeset	292
f3f97841564f Uploaded lecorguille parents: diff changeset	293 -----------------
f3f97841564f Uploaded lecorguille parents: diff changeset	294 Workflow position
f3f97841564f Uploaded lecorguille parents: diff changeset	295 -----------------
f3f97841564f Uploaded lecorguille parents: diff changeset	296
f3f97841564f Uploaded lecorguille parents: diff changeset	297 Upstream tools
f3f97841564f Uploaded lecorguille parents: diff changeset	298
f3f97841564f Uploaded lecorguille parents: diff changeset	299 ========================= ================= =================== ==========
f3f97841564f Uploaded lecorguille parents: diff changeset	300 Name output file format parameter
f3f97841564f Uploaded lecorguille parents: diff changeset	301 ========================= ================= =================== ==========
f3f97841564f Uploaded lecorguille parents: diff changeset	302 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
f3f97841564f Uploaded lecorguille parents: diff changeset	303 ------------------------- ----------------- ------------------- ----------
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	304 xcms.xcmsSet Merger xset.RData rdata.xcms.raw RData file
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	305 ------------------------- ----------------- ------------------- ----------
0 f3f97841564f Uploaded lecorguille parents: diff changeset	306 xcms.retcor xset.RData rdata.xcms.retcor RData file
f3f97841564f Uploaded lecorguille parents: diff changeset	307 ========================= ================= =================== ==========
f3f97841564f Uploaded lecorguille parents: diff changeset	308
f3f97841564f Uploaded lecorguille parents: diff changeset	309
f3f97841564f Uploaded lecorguille parents: diff changeset	310 Downstream tools
f3f97841564f Uploaded lecorguille parents: diff changeset	311
f3f97841564f Uploaded lecorguille parents: diff changeset	312 +---------------------------+--------------------------------------+
f3f97841564f Uploaded lecorguille parents: diff changeset	313 \| Name \| Output file \| Format \|
f3f97841564f Uploaded lecorguille parents: diff changeset	314 +===========================+=================+====================+
f3f97841564f Uploaded lecorguille parents: diff changeset	315 \|xcms.retcor \| xset.RData \| rdata.xcms.group \|
f3f97841564f Uploaded lecorguille parents: diff changeset	316 +---------------------------+--------------------------------------+
f3f97841564f Uploaded lecorguille parents: diff changeset	317 \|xcms.fillPeaks \| xset.RData \| rdata.xcms.group \|
f3f97841564f Uploaded lecorguille parents: diff changeset	318 +---------------------------+--------------------------------------+
f3f97841564f Uploaded lecorguille parents: diff changeset	319
f3f97841564f 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.
f3f97841564f Uploaded lecorguille parents: diff changeset	321
f3f97841564f Uploaded lecorguille parents: diff changeset	322 General schema of the metabolomic workflow
f3f97841564f Uploaded lecorguille parents: diff changeset	323
f3f97841564f Uploaded lecorguille parents: diff changeset	324 .. image:: xcms_group_workflow.png
f3f97841564f Uploaded lecorguille parents: diff changeset	325
f3f97841564f Uploaded lecorguille parents: diff changeset	326
f3f97841564f Uploaded lecorguille parents: diff changeset	327 -----------
f3f97841564f Uploaded lecorguille parents: diff changeset	328 Input files
f3f97841564f Uploaded lecorguille parents: diff changeset	329 -----------
f3f97841564f Uploaded lecorguille parents: diff changeset	330
f3f97841564f Uploaded lecorguille parents: diff changeset	331 +---------------------------+-----------------------+
f3f97841564f Uploaded lecorguille parents: diff changeset	332 \| Parameter : num + label \| Format \|
f3f97841564f Uploaded lecorguille parents: diff changeset	333 +===========================+=======================+
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	334 \| Or : RData file \| rdata.xcms.raw \|
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	335 +---------------------------+-----------------------+
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	336 \| Or : RData file \| rdata.xcms.retcor \|
0 f3f97841564f Uploaded lecorguille parents: diff changeset	337 +---------------------------+-----------------------+
f3f97841564f Uploaded lecorguille parents: diff changeset	338
f3f97841564f Uploaded lecorguille parents: diff changeset	339
f3f97841564f Uploaded lecorguille parents: diff changeset	340 ----------
f3f97841564f Uploaded lecorguille parents: diff changeset	341 Parameters
f3f97841564f Uploaded lecorguille parents: diff changeset	342 ----------
f3f97841564f Uploaded lecorguille parents: diff changeset	343
f3f97841564f Uploaded lecorguille parents: diff changeset	344 Method to use for grouping
f3f97841564f Uploaded lecorguille parents: diff changeset	345 --------------------------
f3f97841564f Uploaded lecorguille parents: diff changeset	346
f3f97841564f Uploaded lecorguille parents: diff changeset	347 mzClust
f3f97841564f Uploaded lecorguille parents: diff changeset	348
f3f97841564f Uploaded lecorguille parents: diff changeset	349 \| Runs high resolution alignment on single spectra samples stored in the RData file generated by the xcmsSet tool.
f3f97841564f Uploaded lecorguille parents: diff changeset	350
f3f97841564f Uploaded lecorguille parents: diff changeset	351 density
f3f97841564f Uploaded lecorguille parents: diff changeset	352
f3f97841564f 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.
f3f97841564f Uploaded lecorguille parents: diff changeset	354
f3f97841564f Uploaded lecorguille parents: diff changeset	355 nearest
f3f97841564f Uploaded lecorguille parents: diff changeset	356
f3f97841564f 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.
f3f97841564f Uploaded lecorguille parents: diff changeset	358
f3f97841564f Uploaded lecorguille parents: diff changeset	359
f3f97841564f Uploaded lecorguille parents: diff changeset	360 ------------
f3f97841564f Uploaded lecorguille parents: diff changeset	361 Output files
f3f97841564f Uploaded lecorguille parents: diff changeset	362 ------------
f3f97841564f Uploaded lecorguille parents: diff changeset	363
f3f97841564f Uploaded lecorguille parents: diff changeset	364 xset.group.Rplots.pdf
f3f97841564f Uploaded lecorguille parents: diff changeset	365
f3f97841564f Uploaded lecorguille parents: diff changeset	366 xset.group.RData: rdata.xcms.group format
f3f97841564f Uploaded lecorguille parents: diff changeset	367
f3f97841564f 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).
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	369
0 f3f97841564f Uploaded lecorguille parents: diff changeset	370
f3f97841564f Uploaded lecorguille parents: diff changeset	371 ------
f3f97841564f Uploaded lecorguille parents: diff changeset	372
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	373 .. class:: infomark
0 f3f97841564f Uploaded lecorguille parents: diff changeset	374
f3f97841564f 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.
f3f97841564f Uploaded lecorguille parents: diff changeset	376
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	377
0 f3f97841564f Uploaded lecorguille parents: diff changeset	378 ---------------------------------------------------
f3f97841564f Uploaded lecorguille parents: diff changeset	379
f3f97841564f Uploaded lecorguille parents: diff changeset	380
f3f97841564f Uploaded lecorguille parents: diff changeset	381 ---------------
f3f97841564f Uploaded lecorguille parents: diff changeset	382 Working example
f3f97841564f Uploaded lecorguille parents: diff changeset	383 ---------------
f3f97841564f Uploaded lecorguille parents: diff changeset	384
f3f97841564f Uploaded lecorguille parents: diff changeset	385 Input files
f3f97841564f Uploaded lecorguille parents: diff changeset	386 -----------
f3f97841564f Uploaded lecorguille parents: diff changeset	387
f3f97841564f Uploaded lecorguille parents: diff changeset	388 \| RData file -> xset.RData
f3f97841564f Uploaded lecorguille parents: diff changeset	389
f3f97841564f Uploaded lecorguille parents: diff changeset	390 Parameters
f3f97841564f Uploaded lecorguille parents: diff changeset	391 ----------
f3f97841564f Uploaded lecorguille parents: diff changeset	392
f3f97841564f Uploaded lecorguille parents: diff changeset	393 \| Method -> density
f3f97841564f Uploaded lecorguille parents: diff changeset	394 \| bw -> 5
f3f97841564f Uploaded lecorguille parents: diff changeset	395 \| minfrac -> 0.3
f3f97841564f Uploaded lecorguille parents: diff changeset	396 \| mzwid -> 0.01
f3f97841564f Uploaded lecorguille parents: diff changeset	397 \| Advanced options: show
f3f97841564f Uploaded lecorguille parents: diff changeset	398 \| max -> 50
f3f97841564f Uploaded lecorguille parents: diff changeset	399
f3f97841564f Uploaded lecorguille parents: diff changeset	400
f3f97841564f Uploaded lecorguille parents: diff changeset	401 Output files
f3f97841564f Uploaded lecorguille parents: diff changeset	402 ------------
f3f97841564f Uploaded lecorguille parents: diff changeset	403
f3f97841564f Uploaded lecorguille parents: diff changeset	404 \| 1) xset.RData: RData file
f3f97841564f Uploaded lecorguille parents: diff changeset	405
f3f97841564f Uploaded lecorguille parents: diff changeset	406 \| 2) Example of an xset.group.Rplots pdf file
f3f97841564f Uploaded lecorguille parents: diff changeset	407
f3f97841564f Uploaded lecorguille parents: diff changeset	408 .. image:: xcms_group.png
f3f97841564f Uploaded lecorguille parents: diff changeset	409 :width: 700
f3f97841564f Uploaded lecorguille parents: diff changeset	410
f3f97841564f Uploaded lecorguille parents: diff changeset	411
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	412 ---------------------------------------------------
2 ed149026836e Uploaded mmonsoor parents: 0 diff changeset	413
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	414 Changelog/News
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	415 --------------
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	416
13 13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	417 Version 2.1.1 - 29/11/2017
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	418
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	419 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	420
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	421 Version 2.1.0 - 07/02/2017
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	422
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	423 - IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	424
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	425 - IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger"
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	426
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	427 - 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
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	428
8 5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 5 diff changeset	429 Version 2.0.6 - 06/07/2016
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 5 diff changeset	430
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 5 diff changeset	431 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 5 diff changeset	432
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	433 Version 2.0.5 - 04/04/2016
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	434
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	435 - TEST: refactoring to pass planemo test using conda dependencies
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	436
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	437
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	438 Version 2.0.4 - 10/02/2016
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	439
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	440 - BUGFIX: better management of errors. Datasets remained green although the process failed
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	441
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	442 - UPDATE: refactoring of internal management of inputs/outputs
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	443
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	444 - UPDATE: refactoring to feed the new report tool
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	445
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	446
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	447 Version 2.0.2 - 02/06/2015
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	448
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	449 - 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.
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	450
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	451 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	452
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	453
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	454 ]]></help>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	455
f3f97841564f Uploaded lecorguille parents: diff changeset	456
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	457 <expand macro="citation" />
0 f3f97841564f Uploaded lecorguille parents: diff changeset	458
f3f97841564f Uploaded lecorguille parents: diff changeset	459
f3f97841564f Uploaded lecorguille parents: diff changeset	460 </tool>

Mercurial > repos > lecorguille > xcms_group

annotate abims_xcms_group.xml @ 13:13558e8a4778 draft