xcms_fillpeaks: abims_xcms_fillPeaks.xml annotate

annotate abims_xcms_fillPeaks.xml @ 30:6b5ed508f81f draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298

author	lecorguille
date	Tue, 13 Feb 2018 04:44:47 -0500
parents	f6d3e6be4ea3
children	8fd5b5afa24d

rev	line source
30 6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.1">
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	2
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	3 <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</description>
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	4
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	5 <macros>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	6 <import>macros.xml</import>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	7 </macros>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	8
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	9 <expand macro="requirements"/>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	10 <expand macro="stdio"/>
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	11
1 107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	12 <command><![CDATA[
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	13 @COMMAND_XCMS_SCRIPT@
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	14 xfunction fillPeaks
22 a6938c381d4e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 20 diff changeset	15 image '$image'
1 107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	16
22 a6938c381d4e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 20 diff changeset	17 xsetRdataOutput '$xsetRData'
1 107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	18
107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	19 method $method
107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	20
20 02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 19 diff changeset	21 @COMMAND_PEAKLIST@
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	22
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	23 @COMMAND_FILE_LOAD@
10 35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82 lecorguille parents: 9 diff changeset	24
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	25 @COMMAND_LOG_EXIT@
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	26
1 107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	27 ]]></command>
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	28
30b01bcefda4 planemo upload lecorguille parents: diff changeset	29 <inputs>
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	30 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" />
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	31 <param name="method" type="select" label="Filling method" help="[method] See the help section below">
30b01bcefda4 planemo upload lecorguille parents: diff changeset	32 <option value="chrom" selected="true">chrom</option>
30b01bcefda4 planemo upload lecorguille parents: diff changeset	33 <option value="MSW" >MSW</option>
30b01bcefda4 planemo upload lecorguille parents: diff changeset	34 </param>
20 02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 19 diff changeset	35
02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 19 diff changeset	36 <expand macro="input_peaklist"/>
02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 19 diff changeset	37
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 22 diff changeset	38 <expand macro="input_file_load"/>
10 35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82 lecorguille parents: 9 diff changeset	39
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	40 </inputs>
30b01bcefda4 planemo upload lecorguille parents: diff changeset	41
30b01bcefda4 planemo upload lecorguille parents: diff changeset	42 <outputs>
30b01bcefda4 planemo upload lecorguille parents: diff changeset	43 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" />
27 0544bc5967ed planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b8ea02b3d37550c33dcf8e099fe8c636287b0865 lecorguille parents: 23 diff changeset	44 <expand macro="output_peaklist" function="fillpeaks" />
1 107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	45 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	46 </outputs>
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	47
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	48 <tests>
9 46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	49 <!--<test>
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	50 <param name="image" value="xset.group.retcor.group.RData"/>
30b01bcefda4 planemo upload lecorguille parents: diff changeset	51 <param name="method" value="chrom"/>
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	52 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" />
1 107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	53 <output name="log">
107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	54 <assert_contents>
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	55 <has_text text="object with 4 samples" />
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	56 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	57 <has_text text="Mass range: 50.0021-999.9863 m/z" />
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	58 <has_text text="Peaks: 199718 (about 49930 per sample)" />
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	59 <has_text text="Peak Groups: 48958" />
1 107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	60 <has_text text="Sample classes: bio, blank" />
107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	61 </assert_contents>
107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	62 </output>
9 46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	63 </test>-->
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	64 <test>
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	65 <param name="image" value="faahKO.xset.group.retcor.group.RData"/>
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	66 <param name="method" value="chrom"/>
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	67 <conditional name="peaklist">
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	68 <param name="convertRTMinute" value="false" />
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	69 <param name="peaklistBool" value="true" />
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	70 <param name="numDigitsMZ" value="4" />
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	71 <param name="numDigitsRT" value="1" />
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	72 </conditional>
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 22 diff changeset	73 <expand macro="test_file_load_zip"/>
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	74 <output name="log">
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	75 <assert_contents>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	76 <has_text text="object with 4 samples" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	77 <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	78 <has_text text="Mass range: 200.1-600 m/z" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	79 <has_text text="Peaks: 32720 (about 8180 per sample)" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	80 <has_text text="Peak Groups: 8157" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	81 <has_text text="Sample classes: KO, WT" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	82 </assert_contents>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	83 </output>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	84 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	85 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	86 </test>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	87 <test>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	88 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData"/>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	89 <param name="method" value="chrom"/>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	90 <conditional name="peaklist">
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	91 <param name="convertRTMinute" value="false" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	92 <param name="peaklistBool" value="true" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	93 <param name="numDigitsMZ" value="4" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	94 <param name="numDigitsRT" value="1" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	95 </conditional>
23 7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 22 diff changeset	96 <expand macro="test_file_load_single"/>
9 46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	97 <output name="log">
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	98 <assert_contents>
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	99 <has_text text="object with 4 samples" />
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	100 <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" />
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	101 <has_text text="Mass range: 200.1-600 m/z" />
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	102 <has_text text="Peaks: 32720 (about 8180 per sample)" />
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	103 <has_text text="Peak Groups: 8157" />
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	104 <has_text text="Sample classes: KO, WT" />
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	105 </assert_contents>
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	106 </output>
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	107 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	108 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	109 </test>
30b01bcefda4 planemo upload lecorguille parents: diff changeset	110 </tests>
30b01bcefda4 planemo upload lecorguille parents: diff changeset	111
1 107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	112 <help><![CDATA[
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	113
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	114 @HELP_AUTHORS@
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	115
30b01bcefda4 planemo upload lecorguille parents: diff changeset	116 ==============
30b01bcefda4 planemo upload lecorguille parents: diff changeset	117 Xcms.fillPeaks
30b01bcefda4 planemo upload lecorguille parents: diff changeset	118 ==============
30b01bcefda4 planemo upload lecorguille parents: diff changeset	119
30 6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	120 -----------
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	121 Description
30b01bcefda4 planemo upload lecorguille parents: diff changeset	122 -----------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	123
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	124 Integrate areas of missing peaks
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	125 For each sample, identify peak groups where that sample is not
30b01bcefda4 planemo upload lecorguille parents: diff changeset	126 represented. For each of those peak groups, integrate the signal
30b01bcefda4 planemo upload lecorguille parents: diff changeset	127 in the region of that peak group and create a new peak.
30b01bcefda4 planemo upload lecorguille parents: diff changeset	128
30b01bcefda4 planemo upload lecorguille parents: diff changeset	129 According to the type of raw-data there are 2
30b01bcefda4 planemo upload lecorguille parents: diff changeset	130 different methods available. for filling gcms/lcms data the method
30b01bcefda4 planemo upload lecorguille parents: diff changeset	131 "chrom" integrates raw-data in the chromatographic domain, whereas
30b01bcefda4 planemo upload lecorguille parents: diff changeset	132 "MSW" is used for peaklists without retention-time information
30b01bcefda4 planemo upload lecorguille parents: diff changeset	133 like those from direct-infusion spectra.
30b01bcefda4 planemo upload lecorguille parents: diff changeset	134
30b01bcefda4 planemo upload lecorguille parents: diff changeset	135
30b01bcefda4 planemo upload lecorguille parents: diff changeset	136
30 6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	137 -----------------
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	138 Workflow position
30b01bcefda4 planemo upload lecorguille parents: diff changeset	139 -----------------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	140
30b01bcefda4 planemo upload lecorguille parents: diff changeset	141
30b01bcefda4 planemo upload lecorguille parents: diff changeset	142 Upstream tools
30b01bcefda4 planemo upload lecorguille parents: diff changeset	143
30 6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	144 ========================= ================= ================== ==========
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	145 Name output file format parameter
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	146 ========================= ================= ================== ==========
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	147 xcms.group xset.group.RData rdata.xcms.group RData file
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	148 ========================= ================= ================== ==========
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	149
30b01bcefda4 planemo upload lecorguille parents: diff changeset	150
30b01bcefda4 planemo upload lecorguille parents: diff changeset	151 Downstream tools
30b01bcefda4 planemo upload lecorguille parents: diff changeset	152
30b01bcefda4 planemo upload lecorguille parents: diff changeset	153 +---------------------------+------------------+-----------------------+
30b01bcefda4 planemo upload lecorguille parents: diff changeset	154 \| Name \| Output file \| Format \|
30b01bcefda4 planemo upload lecorguille parents: diff changeset	155 +===========================+==================+=======================+
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	156 \|CAMERA.annotate \| xset.retcor.RData\| rdata.xcms.fillpeaks \|
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	157 +---------------------------+------------------+-----------------------+
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	158 \|xcms.summary \| xset.retcor.RData\| rdata.xcms.fillpeaks \|
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	159 +---------------------------+------------------+-----------------------+
30b01bcefda4 planemo upload lecorguille parents: diff changeset	160
30 6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	161 The output file xset.fillpeaks is a RData file. You can continue your analysis using it in CAMERA.annotate or xcms.summary tool as a following step of your workflow.
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	162
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	163
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	164 General schema of the metabolomic workflow
30b01bcefda4 planemo upload lecorguille parents: diff changeset	165
30b01bcefda4 planemo upload lecorguille parents: diff changeset	166 .. image:: xcms_fillpeaks_workflow.png
30b01bcefda4 planemo upload lecorguille parents: diff changeset	167
30 6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	168
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	169
30b01bcefda4 planemo upload lecorguille parents: diff changeset	170 -----------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	171 Input files
30b01bcefda4 planemo upload lecorguille parents: diff changeset	172 -----------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	173
30b01bcefda4 planemo upload lecorguille parents: diff changeset	174 +---------------------------+-----------------------+
30b01bcefda4 planemo upload lecorguille parents: diff changeset	175 \| Parameter : num + label \| Format \|
30b01bcefda4 planemo upload lecorguille parents: diff changeset	176 +===========================+=======================+
30b01bcefda4 planemo upload lecorguille parents: diff changeset	177 \| 1 : RData file \| rdata.xcms.group \|
30b01bcefda4 planemo upload lecorguille parents: diff changeset	178 +---------------------------+-----------------------+
30b01bcefda4 planemo upload lecorguille parents: diff changeset	179
30b01bcefda4 planemo upload lecorguille parents: diff changeset	180
30b01bcefda4 planemo upload lecorguille parents: diff changeset	181 ----------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	182 Parameters
30b01bcefda4 planemo upload lecorguille parents: diff changeset	183 ----------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	184
30b01bcefda4 planemo upload lecorguille parents: diff changeset	185
30b01bcefda4 planemo upload lecorguille parents: diff changeset	186 Method
30b01bcefda4 planemo upload lecorguille parents: diff changeset	187 ------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	188
30b01bcefda4 planemo upload lecorguille parents: diff changeset	189 chrom
30b01bcefda4 planemo upload lecorguille parents: diff changeset	190
30b01bcefda4 planemo upload lecorguille parents: diff changeset	191 \| This method produces intensity values for those missing samples by integrating raw data in peak group region. In a given group, the start and ending retention time points for integration are defined by the median start and end points of the other detected peaks. The start and end m/z values are similarly determined. Intensities can be still be zero, which is a rather unusual intensity for a peak. This is the case if e.g. the raw data was threshholded, and the integration area contains no actual raw intensities, or if one sample is miscalibrated, such the raw data points are (just) outside the integration area.
30b01bcefda4 planemo upload lecorguille parents: diff changeset	192 \| Importantly, if retention time correction data is available, the alignment information is used to more precisely integrate the propper region of the raw data. If the corrected retention time is beyond the end of the raw data, the value will be not-a-number (NaN).
30b01bcefda4 planemo upload lecorguille parents: diff changeset	193
30b01bcefda4 planemo upload lecorguille parents: diff changeset	194 MSW
30b01bcefda4 planemo upload lecorguille parents: diff changeset	195
30b01bcefda4 planemo upload lecorguille parents: diff changeset	196 \| "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra.
30b01bcefda4 planemo upload lecorguille parents: diff changeset	197
30 6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	198
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	199 Get a Peak List
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	200 ---------------
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	201
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	202 If 'true', the module generates two additional files corresponding to the peak list:
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	203 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	204 - the data matrix (corresponding to related intensities)
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	205
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	206 decimal places for [mass or retention time] values in identifiers
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	207
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	208 \| Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	209 \| Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	210 \| Theses parameters do not affect decimal places in columns other than the identifier one.
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	211
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	212 Reported intensity values
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	213
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	214 \| This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	215 \| - into: integrated area of original (raw) peak
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	216 \| - maxo: maximum intensity of original (raw) peak
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	217 \| - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	218
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	219 ------------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	220 Output files
30b01bcefda4 planemo upload lecorguille parents: diff changeset	221 ------------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	222
30b01bcefda4 planemo upload lecorguille parents: diff changeset	223 xset.fillPeaks.RData : rdata.xcms.fillpeaks format
30b01bcefda4 planemo upload lecorguille parents: diff changeset	224
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	225 \| Rdata file that will be used in the CAMERA.annotate or xcms.summary step of the workflow.
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	226
30 6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	227 xset.variableMetadata.tsv : tabular format
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	228
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	229 \| Table containing information about ions; can be used as one input of Quality_Metrics or Generic_filter modules.
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	230
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	231 xset.dataMatrix.tsv : tabular format
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	232
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	233 \| Table containing ions' intensities; can be used as one input of Quality_Metrics or Generic_filter modules.
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	234
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	235 ------
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	236
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	237 .. class:: infomark
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	238
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	239 The output file is a xset.fillPeaks.RData file. You can continue your analysis using it in CAMERA.annotate or xcms.summary tool.
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	240
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	241
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	242 ---------------------------------------------------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	243
30b01bcefda4 planemo upload lecorguille parents: diff changeset	244 ---------------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	245 Working example
30b01bcefda4 planemo upload lecorguille parents: diff changeset	246 ---------------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	247
30b01bcefda4 planemo upload lecorguille parents: diff changeset	248 Input files
30b01bcefda4 planemo upload lecorguille parents: diff changeset	249 -----------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	250
30b01bcefda4 planemo upload lecorguille parents: diff changeset	251 \| RData file -> xset.retcor.RData
30b01bcefda4 planemo upload lecorguille parents: diff changeset	252
30b01bcefda4 planemo upload lecorguille parents: diff changeset	253 Parameters
30b01bcefda4 planemo upload lecorguille parents: diff changeset	254 ----------
30b01bcefda4 planemo upload lecorguille parents: diff changeset	255
30 6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	256 \| method -> chrom
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	257 \| Get a Peak List -> false
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	258
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	259
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	260 Output files
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	261 ------------
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	262
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	263 \| xset.fillPeaks.RData: RData file
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	264
30b01bcefda4 planemo upload lecorguille parents: diff changeset	265
5 061958ded240 planemo upload lecorguille parents: 4 diff changeset	266 ---------------------------------------------------
061958ded240 planemo upload lecorguille parents: 4 diff changeset	267
061958ded240 planemo upload lecorguille parents: 4 diff changeset	268 Changelog/News
061958ded240 planemo upload lecorguille parents: 4 diff changeset	269 --------------
061958ded240 planemo upload lecorguille parents: 4 diff changeset	270
30 6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	271 Version 2.1.1 - 29/11/2017
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	272
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	273 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
6b5ed508f81f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 29 diff changeset	274
22 a6938c381d4e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 20 diff changeset	275 Version 2.1.0 - 07/02/2017
20 02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 19 diff changeset	276
02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 19 diff changeset	277 - IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom)
02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 19 diff changeset	278
16 5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	279 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 15 diff changeset	280
15 1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	281 Version 2.0.8 - 22/12/2016
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	282
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	283 - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 12 diff changeset	284
12 1009f0279137 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	285 Version 2.0.7 - 06/07/2016
1009f0279137 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	286
1009f0279137 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	287 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
1009f0279137 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	288
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	289 Version 2.0.6 - 04/04/2016
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	290
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	291 - TEST: refactoring to pass planemo test using conda dependencies
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	292
5 061958ded240 planemo upload lecorguille parents: 4 diff changeset	293 Version 2.0.5 - 10/02/2016
061958ded240 planemo upload lecorguille parents: 4 diff changeset	294
061958ded240 planemo upload lecorguille parents: 4 diff changeset	295 - BUGFIX: better management of errors. Datasets remained green although the process failed
061958ded240 planemo upload lecorguille parents: 4 diff changeset	296
061958ded240 planemo upload lecorguille parents: 4 diff changeset	297 - UPDATE: refactoring of internal management of inputs/outputs
061958ded240 planemo upload lecorguille parents: 4 diff changeset	298
061958ded240 planemo upload lecorguille parents: 4 diff changeset	299 - UPDATE: refactoring to feed the new report tool
061958ded240 planemo upload lecorguille parents: 4 diff changeset	300
061958ded240 planemo upload lecorguille parents: 4 diff changeset	301
061958ded240 planemo upload lecorguille parents: 4 diff changeset	302 Version 2.0.2 - 02/06/2015
061958ded240 planemo upload lecorguille parents: 4 diff changeset	303
061958ded240 planemo upload lecorguille parents: 4 diff changeset	304 - 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.
061958ded240 planemo upload lecorguille parents: 4 diff changeset	305
061958ded240 planemo upload lecorguille parents: 4 diff changeset	306 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
061958ded240 planemo upload lecorguille parents: 4 diff changeset	307
061958ded240 planemo upload lecorguille parents: 4 diff changeset	308
1 107a3de94c05 Uploaded lecorguille parents: 0 diff changeset	309 ]]></help>
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	310
6 f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	311
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	312 <expand macro="citation" />
0 30b01bcefda4 planemo upload lecorguille parents: diff changeset	313
30b01bcefda4 planemo upload lecorguille parents: diff changeset	314
30b01bcefda4 planemo upload lecorguille parents: diff changeset	315 </tool>

Mercurial > repos > lecorguille > xcms_fillpeaks

annotate abims_xcms_fillPeaks.xml @ 30:6b5ed508f81f draft