flashlfq: flashlfq.xml annotate

annotate flashlfq.xml @ 4:597199e75dcc draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376

author	galaxyp
date	Thu, 25 Jan 2018 16:10:39 -0500
parents	41c0c75301b3
children	3b0c2e1927c1

rev	line source
4 597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	1 <tool id="flashlfq" name="FlashLFQ" version="0.1.99">
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>
1 a30802542619 Uploaded galaxyp parents: 0 diff changeset	4 <requirement type="package" version="0.1.99">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"
4 597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	9 ln -s '${idt}' '${idt_path}' &&
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	10 #for $peak_list in $peak_lists:
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	11 #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML"
4 597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	12 ln -s '${peak_list}' '${input_name}' &&
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	13 #end for
4 597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	14
597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	15 FlashLFQ
597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	16 --idt '$idt_path'
597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	17 --rep `pwd`
597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	18 --ppm $ppm
597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	19 --iso $iso
597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	20 --nis $nis
0 8489cc343cde Uploaded galaxyp parents: diff changeset	21 #if $intensity == 'integrate':
4 597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	22 --int true
0 8489cc343cde Uploaded galaxyp parents: diff changeset	23 #end if
8489cc343cde Uploaded galaxyp parents: diff changeset	24 #if $charge == 'precursor':
4 597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	25 --chg true
0 8489cc343cde Uploaded galaxyp parents: diff changeset	26 #end if
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	27 $rmm $mbr
0 8489cc343cde Uploaded galaxyp parents: diff changeset	28 --pau false
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	29 && cat _FlashLFQ_Log.txt \| sed 's/$Analysis summary for:$.working./\1 /' > '$log'
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	30 && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences'
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	31 && cp *_FlashLFQ_QuantifiedModifiedSequences.tsv '$quantifiedModifiedSequences'
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	32 && cp *_FlashLFQ_QuantifiedPeaks.tsv '$quantifiedPeaks'
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	33 && cp *_FlashLFQ_QuantifiedProteins.tsv '$quantifiedProteins'
0 8489cc343cde Uploaded galaxyp parents: diff changeset	34 ]]></command>
8489cc343cde Uploaded galaxyp parents: diff changeset	35 <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	36 <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	37 help="MetaMorpheus,Morpheus"/>
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	38 <param name="peak_lists" type="data" format="mzml" multiple="true" label="spectrum files"/>
0 8489cc343cde Uploaded galaxyp parents: diff changeset	39 <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/>
8489cc343cde Uploaded galaxyp parents: diff changeset	40 <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/>
8489cc343cde Uploaded galaxyp parents: diff changeset	41 <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	42 <param name="intensity" type="select" label="intensity">
8489cc343cde Uploaded galaxyp parents: diff changeset	43 <option value="apex" selected="true">use the apex intensity</option>
8489cc343cde Uploaded galaxyp parents: diff changeset	44 <option value="integrate">integrate chromatographic peak intensity</option>
8489cc343cde Uploaded galaxyp parents: diff changeset	45 </param>
8489cc343cde Uploaded galaxyp parents: diff changeset	46 <param name="charge" type="select" label="charge">
8489cc343cde Uploaded galaxyp parents: diff changeset	47 <option value="all" selected="true">use all identification detected charge states</option>
8489cc343cde Uploaded galaxyp parents: diff changeset	48 <option value="precursor">use precursor charge</option>
8489cc343cde Uploaded galaxyp parents: diff changeset	49 </param>
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	50 <param name="rmm" type="boolean" truevalue="--rmm true" falsevalue="--rmm false" checked="true"
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	51 label="require observed monoisotopic mass peak"/>
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	52 <param name="mbr" type="boolean" truevalue="--mbr true" falsevalue="--mbr false" checked="false"
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	53 label="match between runs"/>
0 8489cc343cde Uploaded galaxyp parents: diff changeset	54 </inputs>
8489cc343cde Uploaded galaxyp parents: diff changeset	55 <outputs>
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	56 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" />
3 41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	57 <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv">
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	58 <actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	59 <action name="column_names" type="metadata"
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	60 default="File Name,Base Sequence,Full Sequence,Protein Group,Peptide Monoisotopic Mass,MS2 Retention Time,Precursor Charge,Theoretical MZ,Peak intensity,Peak RT Start,Peak RT Apex,Peak RT End,Peak MZ,Peak Charge,Num Charge States Observed,Peak Detection Type,PSMs Mapped,Base Sequences Mapped,Full Sequences Mapped,Peak Split Valley RT,Peak Apex Mass Error (ppm)"/>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	61 </actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	62 </data>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	63 <data name="quantifiedBaseSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedBaseSequences.tsv">
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	64 <actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	65 <action name="column_names" type="metadata"
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	66 default="Sequence,Protein Group,${','.join(['Intensity_' + i.name for i in $peak_lists])},${','.join(['Detection Type_' + i.name for i in $peak_lists])}"/>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	67 </actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	68 </data>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	69 <data name="quantifiedModifiedSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedModifiedSequences.tsv">
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	70 <actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	71 <action name="column_names" type="metadata"
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	72 default="Sequence,Protein Group,${','.join(['Intensity_' + i.name for i in $peak_lists])},${','.join(['Detection Type_' + i.name for i in $peak_lists])}"/>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	73 </actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	74 </data>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	75 <data name="quantifiedProteins" format="tabular" label="${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	76 <actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	77 <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	78 default="Protein"/>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	79 </actions>
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	80 </data>
0 8489cc343cde Uploaded galaxyp parents: diff changeset	81 </outputs>
8489cc343cde Uploaded galaxyp parents: diff changeset	82 <tests>
8489cc343cde Uploaded galaxyp parents: diff changeset	83 <test>
8489cc343cde Uploaded galaxyp parents: diff changeset	84 <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	85 <param name="peak_lists" value="sliced-mzml.mzML" ftype="mzml"/>
0 8489cc343cde Uploaded galaxyp parents: diff changeset	86 <param name="ppm" value="12"/>
8489cc343cde Uploaded galaxyp parents: diff changeset	87 <param name="iso" value="6"/>
8489cc343cde Uploaded galaxyp parents: diff changeset	88 <output name="log">
8489cc343cde Uploaded galaxyp parents: diff changeset	89 <assert_contents>
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	90 <has_text text="ppmTolerance = 12" />
0 8489cc343cde Uploaded galaxyp parents: diff changeset	91 <has_text text="isotopePpmTolerance = 6" />
8489cc343cde Uploaded galaxyp parents: diff changeset	92 </assert_contents>
8489cc343cde Uploaded galaxyp parents: diff changeset	93 </output>
8489cc343cde Uploaded galaxyp parents: diff changeset	94 </test>
8489cc343cde Uploaded galaxyp parents: diff changeset	95 </tests>
8489cc343cde Uploaded galaxyp parents: diff changeset	96 <help><![CDATA[
8489cc343cde Uploaded galaxyp parents: diff changeset	97
4 597199e75dcc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376 galaxyp parents: 3 diff changeset	98 FlashLFQ is an ultrafast label-free quantification for mass-spectrometry proteomics.
0 8489cc343cde Uploaded galaxyp parents: diff changeset	99
8489cc343cde Uploaded galaxyp parents: diff changeset	100 Accepted command-line arguments:
8489cc343cde Uploaded galaxyp parents: diff changeset	101
2 d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	102 ::
d042eabcd6ec Uploaded galaxyp parents: 1 diff changeset	103
0 8489cc343cde Uploaded galaxyp parents: diff changeset	104 --idt [string \| identification file path (TSV format)]
8489cc343cde Uploaded galaxyp parents: diff changeset	105 --raw [string \| MS data file (.raw or .mzML)]
8489cc343cde Uploaded galaxyp parents: diff changeset	106 --rep [string \| repository containing MS data files]
8489cc343cde Uploaded galaxyp parents: diff changeset	107 --ppm [double \| monoisotopic ppm tolerance] (default = 10)
8489cc343cde Uploaded galaxyp parents: diff changeset	108 --iso [double \| isotopic distribution tolerance in ppm] (default = 5)
8489cc343cde Uploaded galaxyp parents: diff changeset	109 --sil [boolean \| silent mode; no console output] (default = false)
8489cc343cde Uploaded galaxyp parents: diff changeset	110 --pau [boolean \| pause at end of run] (default = true)
8489cc343cde Uploaded galaxyp parents: diff changeset	111 --int [boolean \| integrate chromatographic peak intensity instead of using
8489cc343cde Uploaded galaxyp parents: diff changeset	112 the apex intensity] (default = false)
8489cc343cde Uploaded galaxyp parents: diff changeset	113 --chg [boolean \| use only precursor charge state; when set to false, FlashLFQ looks
8489cc343cde Uploaded galaxyp parents: diff changeset	114 for all charge states detected in the MS/MS identification file for each peptide] (default = false)
8489cc343cde Uploaded galaxyp parents: diff changeset	115 --mbr [bool\|match between runs]
8489cc343cde Uploaded galaxyp parents: diff changeset	116 --rmm [bool\|require observed monoisotopic mass peak]
8489cc343cde Uploaded galaxyp parents: diff changeset	117 --nis [int\|number of isotopes required to be observed]
8489cc343cde Uploaded galaxyp parents: diff changeset	118
8489cc343cde Uploaded galaxyp parents: diff changeset	119
3 41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	120 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	121
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	122 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	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 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	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 - 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	127 - 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	128 - 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	129 - 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	130 - 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	131 - 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	132 - 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	133
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	134
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	135 Outputs:
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 - 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	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 - 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	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 - 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	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 - 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	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
41c0c75301b3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty galaxyp parents: 2 diff changeset	146 - 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	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
0 8489cc343cde Uploaded galaxyp parents: diff changeset	149 ]]></help>
8489cc343cde Uploaded galaxyp parents: diff changeset	150 <citations>
8489cc343cde Uploaded galaxyp parents: diff changeset	151 <citation type="doi">10.1021/acs.jproteome.7b00608</citation>
8489cc343cde Uploaded galaxyp parents: diff changeset	152 </citations>
8489cc343cde Uploaded galaxyp parents: diff changeset	153 </tool>

Mercurial > repos > galaxyp > flashlfq

annotate flashlfq.xml @ 4:597199e75dcc draft