xcms_group: abims_xcms_group.xml annotate

annotate abims_xcms_group.xml @ 8:5d80e7511dfb draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4

author	lecorguille
date	Wed, 06 Jul 2016 17:42:30 -0400
parents	0306a96cc446
children	c81275aee959

rev	line source
8 5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 5 diff changeset	1 <tool id="abims_xcms_group" name="xcms.group" version="2.0.6">
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@
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	14 xfunction group
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	15 image $image
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	16
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	17 xsetRdataOutput $xsetRData
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	18 rplotspdf $rplotsPdf
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	19
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	20 method $methods.method sleep 0.001
0 f3f97841564f Uploaded lecorguille parents: diff changeset	21 #if $methods.method == "density":
f3f97841564f Uploaded lecorguille parents: diff changeset	22 ## minsamp $methods.minsamp
f3f97841564f Uploaded lecorguille parents: diff changeset	23 minfrac $methods.minfrac
f3f97841564f Uploaded lecorguille parents: diff changeset	24 bw $methods.bw
f3f97841564f Uploaded lecorguille parents: diff changeset	25 mzwid $methods.mzwid
f3f97841564f Uploaded lecorguille parents: diff changeset	26 #if $methods.density_options.option == "show":
f3f97841564f Uploaded lecorguille parents: diff changeset	27 max $methods.density_options.max
f3f97841564f Uploaded lecorguille parents: diff changeset	28 #end if
f3f97841564f Uploaded lecorguille parents: diff changeset	29 #elif $methods.method == "mzClust":
f3f97841564f Uploaded lecorguille parents: diff changeset	30 mzppm $methods.mzppm
f3f97841564f Uploaded lecorguille parents: diff changeset	31 mzabs $methods.mzabs
f3f97841564f Uploaded lecorguille parents: diff changeset	32 minfrac $methods.minfrac
f3f97841564f Uploaded lecorguille parents: diff changeset	33 ## minsamp $methods.minsamp
f3f97841564f Uploaded lecorguille parents: diff changeset	34 #else:
f3f97841564f Uploaded lecorguille parents: diff changeset	35 mzVsRTbalance $methods.mzVsRTbalance
f3f97841564f Uploaded lecorguille parents: diff changeset	36 mzCheck $methods.mzCheck
f3f97841564f Uploaded lecorguille parents: diff changeset	37 rtCheck $methods.rtCheck
f3f97841564f Uploaded lecorguille parents: diff changeset	38 kNN $methods.kNN
f3f97841564f Uploaded lecorguille parents: diff changeset	39 #end if
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	40 @COMMAND_LOG_EXIT@
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	41 ]]></command>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	42
f3f97841564f Uploaded lecorguille parents: diff changeset	43 <inputs>
f3f97841564f Uploaded lecorguille parents: diff changeset	44 <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	45 <conditional name="methods">
f3f97841564f Uploaded lecorguille parents: diff changeset	46 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below">
f3f97841564f Uploaded lecorguille parents: diff changeset	47 <option value="density" selected="true">density</option>
f3f97841564f Uploaded lecorguille parents: diff changeset	48 <option value="mzClust" >mzClust</option>
f3f97841564f Uploaded lecorguille parents: diff changeset	49 <option value="nearest" >nearest</option>
f3f97841564f Uploaded lecorguille parents: diff changeset	50 </param>
f3f97841564f Uploaded lecorguille parents: diff changeset	51 <when value="density">
f3f97841564f Uploaded lecorguille parents: diff changeset	52 <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" />
f3f97841564f Uploaded lecorguille parents: diff changeset	53 <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	54 <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	55 <!--
f3f97841564f Uploaded lecorguille parents: diff changeset	56 <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 " />
f3f97841564f Uploaded lecorguille parents: diff changeset	57 -->
f3f97841564f Uploaded lecorguille parents: diff changeset	58 <conditional name="density_options">
f3f97841564f Uploaded lecorguille parents: diff changeset	59 <param name="option" type="select" label="Advanced options">
f3f97841564f Uploaded lecorguille parents: diff changeset	60 <option value="show">show</option>
f3f97841564f Uploaded lecorguille parents: diff changeset	61 <option value="hide" selected="true">hide</option>
f3f97841564f Uploaded lecorguille parents: diff changeset	62 </param>
f3f97841564f Uploaded lecorguille parents: diff changeset	63 <when value="show">
f3f97841564f Uploaded lecorguille parents: diff changeset	64 <param name="max" type="integer" value="5" label="Maximum number of groups to identify in a single m/z slice" help="[max]" />
f3f97841564f Uploaded lecorguille parents: diff changeset	65 </when>
f3f97841564f Uploaded lecorguille parents: diff changeset	66 <when value="hide">
f3f97841564f Uploaded lecorguille parents: diff changeset	67 </when>
f3f97841564f Uploaded lecorguille parents: diff changeset	68 </conditional>
f3f97841564f Uploaded lecorguille parents: diff changeset	69
f3f97841564f Uploaded lecorguille parents: diff changeset	70 </when>
f3f97841564f Uploaded lecorguille parents: diff changeset	71 <when value="mzClust">
f3f97841564f Uploaded lecorguille parents: diff changeset	72 <param name="mzppm" type="integer" value="20 " label="Relative error used for clustering/grouping in ppm" help="[mzppm]" />
f3f97841564f Uploaded lecorguille parents: diff changeset	73 <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" />
f3f97841564f Uploaded lecorguille parents: diff changeset	74 <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	75 <!--
f3f97841564f Uploaded lecorguille parents: diff changeset	76 <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 " />
f3f97841564f Uploaded lecorguille parents: diff changeset	77 -->
f3f97841564f Uploaded lecorguille parents: diff changeset	78 </when>
f3f97841564f Uploaded lecorguille parents: diff changeset	79 <when value="nearest">
f3f97841564f Uploaded lecorguille parents: diff changeset	80 <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	81 <param name="mzCheck" type="float" value="0.2" label="Maximum tolerated distance for mz" help="[mzCheck]" />
f3f97841564f Uploaded lecorguille parents: diff changeset	82 <param name="rtCheck" type="integer" value="15" label="Maximum tolerated distance for RT" help="[rtCheck]" />
f3f97841564f Uploaded lecorguille parents: diff changeset	83 <param name="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" help="[kNN]" />
f3f97841564f Uploaded lecorguille parents: diff changeset	84 </when>
f3f97841564f Uploaded lecorguille parents: diff changeset	85 </conditional>
f3f97841564f Uploaded lecorguille parents: diff changeset	86 <!--
f3f97841564f Uploaded lecorguille parents: diff changeset	87 <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">
f3f97841564f Uploaded lecorguille parents: diff changeset	88 <validator type="in_range" message="Must be more than 0" min="0.001" max="inf"/>
f3f97841564f Uploaded lecorguille parents: diff changeset	89 </param>
f3f97841564f Uploaded lecorguille parents: diff changeset	90 -->
f3f97841564f Uploaded lecorguille parents: diff changeset	91
f3f97841564f Uploaded lecorguille parents: diff changeset	92 </inputs>
f3f97841564f Uploaded lecorguille parents: diff changeset	93
f3f97841564f Uploaded lecorguille parents: diff changeset	94 <outputs>
f3f97841564f Uploaded lecorguille parents: diff changeset	95 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
f3f97841564f Uploaded lecorguille parents: diff changeset	96 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	97 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
0 f3f97841564f Uploaded lecorguille parents: diff changeset	98 </outputs>
f3f97841564f Uploaded lecorguille parents: diff changeset	99
f3f97841564f Uploaded lecorguille parents: diff changeset	100 <tests>
5 0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	101 <!--<test>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	102 <param name="image" value="xset.RData"/>
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	103 <param name="methods\|method" value="density"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	104 <param name="methods\|bw" value="5"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	105 <param name="methods\|minfrac" value="0.3"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	106 <param name="methods\|mzwid" value="0.01"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	107 <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	108 <param name="methods\|density_options\|max" value="50"/>
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	109 <output name="log">
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	110 <assert_contents>
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	111 <has_text text="object with 4 samples" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	112 <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	113 <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	114 <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	115 <has_text text="Peak Groups: 48998" />
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	116 <has_text text="Sample classes: bio, blank" />
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	117 </assert_contents>
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	118 </output>
5 0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	119 </test>-->
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	120 <test>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	121 <param name="image" value="faahKO.xset.RData"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	122 <param name="methods\|method" value="density"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	123 <param name="methods\|bw" value="5"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	124 <param name="methods\|minfrac" value="0.3"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	125 <param name="methods\|mzwid" value="0.01"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	126 <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	127 <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	128 <output name="log">
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	129 <assert_contents>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	130 <has_text text="object with 4 samples" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	131 <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	132 <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	133 <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	134 <has_text text="Peak Groups: 8275" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	135 <has_text text="Sample classes: KO, WT" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	136 </assert_contents>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	137 </output>
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	138 </test>
5 0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	139 <!--<test>
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	140 <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	141 <param name="methods\|method" value="density"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	142 <param name="methods\|bw" value="5"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	143 <param name="methods\|minfrac" value="0.3"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	144 <param name="methods\|mzwid" value="0.01"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	145 <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	146 <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	147 <output name="log">
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	148 <assert_contents>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	149 <has_text text="object with 4 samples" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	150 <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	151 <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	152 <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	153 <has_text text="Peak Groups: 48958" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	154 <has_text text="Sample classes: bio, blank" />
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	155 </assert_contents>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	156 </output>
5 0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	157 </test>-->
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	158 <test>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	159 <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	160 <param name="methods\|method" value="density"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	161 <param name="methods\|bw" value="5"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	162 <param name="methods\|minfrac" value="0.3"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	163 <param name="methods\|mzwid" value="0.01"/>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	164 <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	165 <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	166 <output name="log">
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	167 <assert_contents>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	168 <has_text text="object with 4 samples" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	169 <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	170 <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	171 <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	172 <has_text text="Peak Groups: 8157" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	173 <has_text text="Sample classes: KO, WT" />
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	174 </assert_contents>
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	175 </output>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	176 </test>
f3f97841564f Uploaded lecorguille parents: diff changeset	177 </tests>
f3f97841564f Uploaded lecorguille parents: diff changeset	178
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	179 <help><![CDATA[
0 f3f97841564f Uploaded lecorguille parents: diff changeset	180
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	181 @HELP_AUTHORS@
0 f3f97841564f Uploaded lecorguille parents: diff changeset	182
f3f97841564f Uploaded lecorguille parents: diff changeset	183 ==========
f3f97841564f Uploaded lecorguille parents: diff changeset	184 Xcms.Group
f3f97841564f Uploaded lecorguille parents: diff changeset	185 ==========
f3f97841564f Uploaded lecorguille parents: diff changeset	186
f3f97841564f Uploaded lecorguille parents: diff changeset	187 -----------
f3f97841564f Uploaded lecorguille parents: diff changeset	188 Description
f3f97841564f Uploaded lecorguille parents: diff changeset	189 -----------
f3f97841564f Uploaded lecorguille parents: diff changeset	190
f3f97841564f Uploaded lecorguille parents: diff changeset	191 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	192
f3f97841564f Uploaded lecorguille parents: diff changeset	193
f3f97841564f Uploaded lecorguille parents: diff changeset	194
f3f97841564f Uploaded lecorguille parents: diff changeset	195 -----------------
f3f97841564f Uploaded lecorguille parents: diff changeset	196 Workflow position
f3f97841564f Uploaded lecorguille parents: diff changeset	197 -----------------
f3f97841564f Uploaded lecorguille parents: diff changeset	198
f3f97841564f Uploaded lecorguille parents: diff changeset	199 Upstream tools
f3f97841564f Uploaded lecorguille parents: diff changeset	200
f3f97841564f Uploaded lecorguille parents: diff changeset	201 ========================= ================= =================== ==========
f3f97841564f Uploaded lecorguille parents: diff changeset	202 Name output file format parameter
f3f97841564f Uploaded lecorguille parents: diff changeset	203 ========================= ================= =================== ==========
f3f97841564f Uploaded lecorguille parents: diff changeset	204 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
f3f97841564f Uploaded lecorguille parents: diff changeset	205 ------------------------- ----------------- ------------------- ----------
f3f97841564f Uploaded lecorguille parents: diff changeset	206 xcms.retcor xset.RData rdata.xcms.retcor RData file
f3f97841564f Uploaded lecorguille parents: diff changeset	207 ========================= ================= =================== ==========
f3f97841564f Uploaded lecorguille parents: diff changeset	208
f3f97841564f Uploaded lecorguille parents: diff changeset	209
f3f97841564f Uploaded lecorguille parents: diff changeset	210 Downstream tools
f3f97841564f Uploaded lecorguille parents: diff changeset	211
f3f97841564f Uploaded lecorguille parents: diff changeset	212 +---------------------------+--------------------------------------+
f3f97841564f Uploaded lecorguille parents: diff changeset	213 \| Name \| Output file \| Format \|
f3f97841564f Uploaded lecorguille parents: diff changeset	214 +===========================+=================+====================+
f3f97841564f Uploaded lecorguille parents: diff changeset	215 \|xcms.retcor \| xset.RData \| rdata.xcms.group \|
f3f97841564f Uploaded lecorguille parents: diff changeset	216 +---------------------------+--------------------------------------+
f3f97841564f Uploaded lecorguille parents: diff changeset	217 \|xcms.fillPeaks \| xset.RData \| rdata.xcms.group \|
f3f97841564f Uploaded lecorguille parents: diff changeset	218 +---------------------------+--------------------------------------+
f3f97841564f Uploaded lecorguille parents: diff changeset	219
f3f97841564f Uploaded lecorguille parents: diff changeset	220 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	221
f3f97841564f Uploaded lecorguille parents: diff changeset	222 General schema of the metabolomic workflow
f3f97841564f Uploaded lecorguille parents: diff changeset	223
f3f97841564f Uploaded lecorguille parents: diff changeset	224 .. image:: xcms_group_workflow.png
f3f97841564f Uploaded lecorguille parents: diff changeset	225
f3f97841564f Uploaded lecorguille parents: diff changeset	226
f3f97841564f Uploaded lecorguille parents: diff changeset	227 -----------
f3f97841564f Uploaded lecorguille parents: diff changeset	228 Input files
f3f97841564f Uploaded lecorguille parents: diff changeset	229 -----------
f3f97841564f Uploaded lecorguille parents: diff changeset	230
f3f97841564f Uploaded lecorguille parents: diff changeset	231 +---------------------------+-----------------------+
f3f97841564f Uploaded lecorguille parents: diff changeset	232 \| Parameter : num + label \| Format \|
f3f97841564f Uploaded lecorguille parents: diff changeset	233 +===========================+=======================+
f3f97841564f Uploaded lecorguille parents: diff changeset	234 \| 1 : RData file \| rdata.xcms.group \|
f3f97841564f Uploaded lecorguille parents: diff changeset	235 +---------------------------+-----------------------+
f3f97841564f Uploaded lecorguille parents: diff changeset	236
f3f97841564f Uploaded lecorguille parents: diff changeset	237
f3f97841564f Uploaded lecorguille parents: diff changeset	238 ----------
f3f97841564f Uploaded lecorguille parents: diff changeset	239 Parameters
f3f97841564f Uploaded lecorguille parents: diff changeset	240 ----------
f3f97841564f Uploaded lecorguille parents: diff changeset	241
f3f97841564f Uploaded lecorguille parents: diff changeset	242 Method to use for grouping
f3f97841564f Uploaded lecorguille parents: diff changeset	243 --------------------------
f3f97841564f Uploaded lecorguille parents: diff changeset	244
f3f97841564f Uploaded lecorguille parents: diff changeset	245 mzClust
f3f97841564f Uploaded lecorguille parents: diff changeset	246
f3f97841564f Uploaded lecorguille parents: diff changeset	247 \| Runs high resolution alignment on single spectra samples stored in the RData file generated by the xcmsSet tool.
f3f97841564f Uploaded lecorguille parents: diff changeset	248
f3f97841564f Uploaded lecorguille parents: diff changeset	249 density
f3f97841564f Uploaded lecorguille parents: diff changeset	250
f3f97841564f Uploaded lecorguille parents: diff changeset	251 \| 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	252
f3f97841564f Uploaded lecorguille parents: diff changeset	253 nearest
f3f97841564f Uploaded lecorguille parents: diff changeset	254
f3f97841564f Uploaded lecorguille parents: diff changeset	255 \| 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	256
f3f97841564f Uploaded lecorguille parents: diff changeset	257
f3f97841564f Uploaded lecorguille parents: diff changeset	258 ------------
f3f97841564f Uploaded lecorguille parents: diff changeset	259 Output files
f3f97841564f Uploaded lecorguille parents: diff changeset	260 ------------
f3f97841564f Uploaded lecorguille parents: diff changeset	261
f3f97841564f Uploaded lecorguille parents: diff changeset	262 xset.group.Rplots.pdf
f3f97841564f Uploaded lecorguille parents: diff changeset	263
f3f97841564f Uploaded lecorguille parents: diff changeset	264 xset.group.RData: rdata.xcms.group format
f3f97841564f Uploaded lecorguille parents: diff changeset	265
f3f97841564f Uploaded lecorguille parents: diff changeset	266 \| Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks).
f3f97841564f Uploaded lecorguille parents: diff changeset	267
f3f97841564f Uploaded lecorguille parents: diff changeset	268
f3f97841564f Uploaded lecorguille parents: diff changeset	269 ------
f3f97841564f Uploaded lecorguille parents: diff changeset	270
f3f97841564f Uploaded lecorguille parents: diff changeset	271 .. class:: infomark
f3f97841564f Uploaded lecorguille parents: diff changeset	272
f3f97841564f Uploaded lecorguille parents: diff changeset	273 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	274
f3f97841564f Uploaded lecorguille parents: diff changeset	275
f3f97841564f Uploaded lecorguille parents: diff changeset	276 ---------------------------------------------------
f3f97841564f Uploaded lecorguille parents: diff changeset	277
f3f97841564f Uploaded lecorguille parents: diff changeset	278
f3f97841564f Uploaded lecorguille parents: diff changeset	279 ---------------
f3f97841564f Uploaded lecorguille parents: diff changeset	280 Working example
f3f97841564f Uploaded lecorguille parents: diff changeset	281 ---------------
f3f97841564f Uploaded lecorguille parents: diff changeset	282
f3f97841564f Uploaded lecorguille parents: diff changeset	283 Input files
f3f97841564f Uploaded lecorguille parents: diff changeset	284 -----------
f3f97841564f Uploaded lecorguille parents: diff changeset	285
f3f97841564f Uploaded lecorguille parents: diff changeset	286 \| RData file -> xset.RData
f3f97841564f Uploaded lecorguille parents: diff changeset	287
f3f97841564f Uploaded lecorguille parents: diff changeset	288 Parameters
f3f97841564f Uploaded lecorguille parents: diff changeset	289 ----------
f3f97841564f Uploaded lecorguille parents: diff changeset	290
f3f97841564f Uploaded lecorguille parents: diff changeset	291 \| Method -> density
f3f97841564f Uploaded lecorguille parents: diff changeset	292 \| bw -> 5
f3f97841564f Uploaded lecorguille parents: diff changeset	293 \| minfrac -> 0.3
f3f97841564f Uploaded lecorguille parents: diff changeset	294 \| mzwid -> 0.01
f3f97841564f Uploaded lecorguille parents: diff changeset	295 \| Advanced options: show
f3f97841564f Uploaded lecorguille parents: diff changeset	296 \| max -> 50
f3f97841564f Uploaded lecorguille parents: diff changeset	297
f3f97841564f Uploaded lecorguille parents: diff changeset	298
f3f97841564f Uploaded lecorguille parents: diff changeset	299 Output files
f3f97841564f Uploaded lecorguille parents: diff changeset	300 ------------
f3f97841564f Uploaded lecorguille parents: diff changeset	301
f3f97841564f Uploaded lecorguille parents: diff changeset	302 \| 1) xset.RData: RData file
f3f97841564f Uploaded lecorguille parents: diff changeset	303
f3f97841564f Uploaded lecorguille parents: diff changeset	304 \| 2) Example of an xset.group.Rplots pdf file
f3f97841564f Uploaded lecorguille parents: diff changeset	305
f3f97841564f Uploaded lecorguille parents: diff changeset	306 .. image:: xcms_group.png
f3f97841564f Uploaded lecorguille parents: diff changeset	307 :width: 700
f3f97841564f Uploaded lecorguille parents: diff changeset	308
f3f97841564f Uploaded lecorguille parents: diff changeset	309
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	310 ---------------------------------------------------
2 ed149026836e Uploaded mmonsoor parents: 0 diff changeset	311
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	312 Changelog/News
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	313 --------------
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	314
8 5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 5 diff changeset	315 Version 2.0.6 - 06/07/2016
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 5 diff changeset	316
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 5 diff changeset	317 - 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	318
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	319 Version 2.0.5 - 04/04/2016
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	320
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	321 - TEST: refactoring to pass planemo test using conda dependencies
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	322
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	323
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	324 Version 2.0.4 - 10/02/2016
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	325
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	326 - BUGFIX: better management of errors. Datasets remained green although the process failed
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	327
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	328 - UPDATE: refactoring of internal management of inputs/outputs
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	329
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	330 - UPDATE: refactoring to feed the new report tool
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	331
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	332
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	333 Version 2.0.2 - 02/06/2015
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	334
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	335 - 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	336
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	337 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	338
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	339
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	340 ]]></help>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	341
f3f97841564f Uploaded lecorguille parents: diff changeset	342
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	343 <expand macro="citation" />
0 f3f97841564f Uploaded lecorguille parents: diff changeset	344
f3f97841564f Uploaded lecorguille parents: diff changeset	345
f3f97841564f Uploaded lecorguille parents: diff changeset	346 </tool>

Mercurial > repos > lecorguille > xcms_group

annotate abims_xcms_group.xml @ 8:5d80e7511dfb draft