flashlfq: flashlfq.xml annotate

annotate flashlfq.xml @ 8:69cd4ab3145b draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 4b7c3ac13ae2d5d3b18784c580218f39ed7de6e1

author	galaxyp
date	Fri, 26 Jan 2018 09:07:49 -0500
parents	c4c61493c9a8
children	944d155c01c9

rev	line source
8 69cd4ab3145b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 4b7c3ac13ae2d5d3b18784c580218f39ed7de6e1 galaxyp parents: 7 diff changeset	1 <tool id="flashlfq" name="FlashLFQ" version="0.1.100">
0 8489cc343cde Uploaded galaxyp parents: diff changeset	2 <description>ultrafast label-free quantification for mass-spectrometry proteomics</description>
8489cc343cde Uploaded galaxyp parents: diff changeset	3 <requirements>
8 69cd4ab3145b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 4b7c3ac13ae2d5d3b18784c580218f39ed7de6e1 galaxyp parents: 7 diff changeset	4 <requirement type="package" version="0.1.100">flashlfq</requirement>
0 8489cc343cde Uploaded galaxyp parents: diff changeset	5 </requirements>
8489cc343cde Uploaded galaxyp parents: diff changeset	6 <command><![CDATA[
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	7 #import re
3 41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	8 #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv"
6 279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	9 ln -s '${idt}' '${idt_path}' &&
279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	10 mkdir spectrum_dir &&
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	11 #for $peak_list in $peak_lists:
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	12 #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML"
6 279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	13 ln -s '${peak_list}' 'spectrum_dir/${input_name}' &&
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	14 #end for
6 279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	15
279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	16 FlashLFQ
279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	17 --idt '$idt_path'
279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	18 --rep spectrum_dir
279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	19 --ppm $ppm
279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	20 --iso $iso
279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	21 --nis $nis
0 8489cc343cde Uploaded galaxyp parents: diff changeset	22 #if $intensity == 'integrate':
6 279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	23 --int true
0 8489cc343cde Uploaded galaxyp parents: diff changeset	24 #end if
8489cc343cde Uploaded galaxyp parents: diff changeset	25 #if $charge == 'precursor':
6 279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	26 --chg true
0 8489cc343cde Uploaded galaxyp parents: diff changeset	27 #end if
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	28 $rmm $mbr
0 8489cc343cde Uploaded galaxyp parents: diff changeset	29 --pau false
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	30 && cat _FlashLFQ_Log.txt \| sed 's/$Analysis summary for:$.working./\1 /' > '$log'
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	31 && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences'
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	32 && cp *_FlashLFQ_QuantifiedModifiedSequences.tsv '$quantifiedModifiedSequences'
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	33 && cp *_FlashLFQ_QuantifiedPeaks.tsv '$quantifiedPeaks'
7 c4c61493c9a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 38eecdb36b6b505afcdd99de7351eed9c3729843 galaxyp parents: 6 diff changeset	34 ## create issue for FlashLFQ to name column headers correctly
c4c61493c9a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 38eecdb36b6b505afcdd99de7351eed9c3729843 galaxyp parents: 6 diff changeset	35 && grep -v '^test$' *_FlashLFQ_QuantifiedProteins.tsv > '$quantifiedProteins'
0 8489cc343cde Uploaded galaxyp parents: diff changeset	36 ]]></command>
8489cc343cde Uploaded galaxyp parents: diff changeset	37 <inputs>
3 41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	38 <param name="idt" type="data" format="tabular" label="identification file"
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	39 help="MetaMorpheus,Morpheus"/>
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	40 <param name="peak_lists" type="data" format="mzml" multiple="true" label="spectrum files"/>
0 8489cc343cde Uploaded galaxyp parents: diff changeset	41 <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/>
8489cc343cde Uploaded galaxyp parents: diff changeset	42 <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/>
8489cc343cde Uploaded galaxyp parents: diff changeset	43 <param name="nis" type="integer" value="2" min="1" max="30" label="number of isotopes required to be observed"/>
8489cc343cde Uploaded galaxyp parents: diff changeset	44 <param name="intensity" type="select" label="intensity">
8489cc343cde Uploaded galaxyp parents: diff changeset	45 <option value="apex" selected="true">use the apex intensity</option>
8489cc343cde Uploaded galaxyp parents: diff changeset	46 <option value="integrate">integrate chromatographic peak intensity</option>
8489cc343cde Uploaded galaxyp parents: diff changeset	47 </param>
8489cc343cde Uploaded galaxyp parents: diff changeset	48 <param name="charge" type="select" label="charge">
8489cc343cde Uploaded galaxyp parents: diff changeset	49 <option value="all" selected="true">use all identification detected charge states</option>
8489cc343cde Uploaded galaxyp parents: diff changeset	50 <option value="precursor">use precursor charge</option>
8489cc343cde Uploaded galaxyp parents: diff changeset	51 </param>
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	52 <param name="rmm" type="boolean" truevalue="--rmm true" falsevalue="--rmm false" checked="true"
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	53 label="require observed monoisotopic mass peak"/>
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	54 <param name="mbr" type="boolean" truevalue="--mbr true" falsevalue="--mbr false" checked="false"
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	55 label="match between runs"/>
0 8489cc343cde Uploaded galaxyp parents: diff changeset	56 </inputs>
8489cc343cde Uploaded galaxyp parents: diff changeset	57 <outputs>
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	58 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" />
3 41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	59 <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv">
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	60 <actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	61 <action name="column_names" type="metadata"
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	62 default="File Name,Base Sequence,Full Sequence,Protein Group,Peptide Monoisotopic Mass,MS2 Retention Time,Precursor Charge,Theoretical MZ,Peak intensity,Peak RT Start,Peak RT Apex,Peak RT End,Peak MZ,Peak Charge,Num Charge States Observed,Peak Detection Type,PSMs Mapped,Base Sequences Mapped,Full Sequences Mapped,Peak Split Valley RT,Peak Apex Mass Error (ppm)"/>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	63 </actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	64 </data>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	65 <data name="quantifiedBaseSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedBaseSequences.tsv">
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	66 <actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	67 <action name="column_names" type="metadata"
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	68 default="Sequence,Protein Group,${','.join(['Intensity_' + i.name for i in $peak_lists])},${','.join(['Detection Type_' + i.name for i in $peak_lists])}"/>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	69 </actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	70 </data>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	71 <data name="quantifiedModifiedSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedModifiedSequences.tsv">
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	72 <actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	73 <action name="column_names" type="metadata"
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	74 default="Sequence,Protein Group,${','.join(['Intensity_' + i.name for i in $peak_lists])},${','.join(['Detection Type_' + i.name for i in $peak_lists])}"/>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	75 </actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	76 </data>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	77 <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv">
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	78 <actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	79 <action name="column_names" type="metadata"
7 c4c61493c9a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 38eecdb36b6b505afcdd99de7351eed9c3729843 galaxyp parents: 6 diff changeset	80 default="Protein,${','.join([i.name for i in $peak_lists])}"/>
3 41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	81 </actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	82 </data>
0 8489cc343cde Uploaded galaxyp parents: diff changeset	83 </outputs>
8489cc343cde Uploaded galaxyp parents: diff changeset	84 <tests>
8489cc343cde Uploaded galaxyp parents: diff changeset	85 <test>
8489cc343cde Uploaded galaxyp parents: diff changeset	86 <param name="idt" value="aggregatePSMs_5ppmAroundZero.psmtsv" ftype="tabular"/>
3 41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	87 <param name="peak_lists" value="sliced-mzml.mzML" ftype="mzml"/>
0 8489cc343cde Uploaded galaxyp parents: diff changeset	88 <param name="ppm" value="12"/>
8489cc343cde Uploaded galaxyp parents: diff changeset	89 <param name="iso" value="6"/>
8489cc343cde Uploaded galaxyp parents: diff changeset	90 <output name="log">
8489cc343cde Uploaded galaxyp parents: diff changeset	91 <assert_contents>
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	92 <has_text text="ppmTolerance = 12" />
0 8489cc343cde Uploaded galaxyp parents: diff changeset	93 <has_text text="isotopePpmTolerance = 6" />
8489cc343cde Uploaded galaxyp parents: diff changeset	94 </assert_contents>
8489cc343cde Uploaded galaxyp parents: diff changeset	95 </output>
8489cc343cde Uploaded galaxyp parents: diff changeset	96 </test>
8489cc343cde Uploaded galaxyp parents: diff changeset	97 </tests>
8489cc343cde Uploaded galaxyp parents: diff changeset	98 <help><![CDATA[
8489cc343cde Uploaded galaxyp parents: diff changeset	99
6 279fbc8ad992 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de galaxyp parents: 5 diff changeset	100 FlashLFQ is an ultrafast label-free quantification for mass-spectrometry proteomics.
0 8489cc343cde Uploaded galaxyp parents: diff changeset	101
8489cc343cde Uploaded galaxyp parents: diff changeset	102 Accepted command-line arguments:
8489cc343cde Uploaded galaxyp parents: diff changeset	103
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	104 ::
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	105
0 8489cc343cde Uploaded galaxyp parents: diff changeset	106 --idt [string \| identification file path (TSV format)]
8489cc343cde Uploaded galaxyp parents: diff changeset	107 --raw [string \| MS data file (.raw or .mzML)]
8489cc343cde Uploaded galaxyp parents: diff changeset	108 --rep [string \| repository containing MS data files]
8489cc343cde Uploaded galaxyp parents: diff changeset	109 --ppm [double \| monoisotopic ppm tolerance] (default = 10)
8489cc343cde Uploaded galaxyp parents: diff changeset	110 --iso [double \| isotopic distribution tolerance in ppm] (default = 5)
8489cc343cde Uploaded galaxyp parents: diff changeset	111 --sil [boolean \| silent mode; no console output] (default = false)
8489cc343cde Uploaded galaxyp parents: diff changeset	112 --pau [boolean \| pause at end of run] (default = true)
8489cc343cde Uploaded galaxyp parents: diff changeset	113 --int [boolean \| integrate chromatographic peak intensity instead of using
8489cc343cde Uploaded galaxyp parents: diff changeset	114 the apex intensity] (default = false)
8489cc343cde Uploaded galaxyp parents: diff changeset	115 --chg [boolean \| use only precursor charge state; when set to false, FlashLFQ looks
8489cc343cde Uploaded galaxyp parents: diff changeset	116 for all charge states detected in the MS/MS identification file for each peptide] (default = false)
8489cc343cde Uploaded galaxyp parents: diff changeset	117 --mbr [bool\|match between runs]
8489cc343cde Uploaded galaxyp parents: diff changeset	118 --rmm [bool\|require observed monoisotopic mass peak]
8489cc343cde Uploaded galaxyp parents: diff changeset	119 --nis [int\|number of isotopes required to be observed]
8489cc343cde Uploaded galaxyp parents: diff changeset	120
8489cc343cde Uploaded galaxyp parents: diff changeset	121
3 41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	122 Tab-Delimited Identification Text File
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	123
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	124 The first line of the text file should contain column headers identifying what each column is. Note that MetaMorpheus (.psmtsv), Morpheus, MaxQuant (msms.txt), and TDPortal tab-delimited column headers are supported natively and such files can be read without modification. For search software that lists decoys and PSMs above 1% FDR (e.g., MetaMorpheus), you may want to remove these prior to FlashLFQ analysis. FlashLFQ will probably crash if ambiguous PSMs are passed into it (e.g., a PSM with more than 2 peptides listed in one line).
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	125
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	126 The following headers are required in the list of MS/MS identifications:
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	127
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	128 - File Name - File extensions should be tolerated, but no extension is tested more extensively (e.g. use MyFile and not MyFile.mzML)
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	129 - Base Sequence - Should only contain amino acid sequences, or it will likely result in a crash
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	130 - Full Sequence - Modified sequence. Can contain any letters, but must be consistent between the same peptidoform to get accurate results
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	131 - Peptide Monoisotopic Mass - Theoretical monoisotopic mass, including modification mass
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	132 - Scan Retention Time - MS/MS identification scan retention time
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	133 - Precursor Charge - Charge of the ion selected for MS/MS resulting in the identification
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	134 - Protein Accession - Protein accession(s) for the peptide; protein quantification is still preliminary
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	135
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	136
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	137 Outputs:
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	138
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	139 - QuantifiedProteins.tsv - Protein intensities are summed here within a run.
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	140
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	141 - QuantifiedPeaks.tsv - Each chromatographic peak is shown here, even peaks that were not quantifiable (peak intensity = 0). Details about each peak, such as number of PSMs mapped, start/apex/end retention times, ppm error, etc are contained in this file. A peptide can have multiple peaks over the course of a run (e.g., oxidized peptidoforms elute at different times, etc). Ambiguous peaks are displayed with a \| (pipe) delimiter to indicate more than one peptide mapped to that peak.
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	142
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	143 - QuantifiedModifiedSequences.tsv - Similar to QuantifiedBaseSequences, but instead of being summed by Base Sequence, peptide intensities are summed by modified sequence; this makes it convenient to compare modified peptidoform intensities across runs.
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	144
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	145 - QuantifiedBaseSequences.tsv - Peptide intensities are summed here within a run (including differently-modified forms of the same amino acid sequence) and displayed in a convenient format for comparing across runs. The identification type (MS/MS or MBR) is also indicated. A peptide with more than 30% of its intensity coming from ambiguous peak(s) is considered not quantifiable and is given an intensity of -1.
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	146
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	147
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	148 - Log.txt - Log of the FlashLFQ run. Includes timestamps and quantification time for each file, total analysis time, directories used, and settings.
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	149
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	150
0 8489cc343cde Uploaded galaxyp parents: diff changeset	151 ]]></help>
8489cc343cde Uploaded galaxyp parents: diff changeset	152 <citations>
8489cc343cde Uploaded galaxyp parents: diff changeset	153 <citation type="doi">10.1021/acs.jproteome.7b00608</citation>
8489cc343cde Uploaded galaxyp parents: diff changeset	154 </citations>
8489cc343cde Uploaded galaxyp parents: diff changeset	155 </tool>

Mercurial > repos > galaxyp > flashlfq

annotate flashlfq.xml @ 8:69cd4ab3145b draft