dimspy_process_scans: process

annotate process_scans.xml @ 2:bc099f2346a1 draft default tip

"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448"

author	computational-metabolomics
date	Wed, 17 Feb 2021 10:57:11 +0000
parents	deafa30d6570
children

rev	line source
2 bc099f2346a1 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448" computational-metabolomics parents: 1 diff changeset	1 <tool id="dimspy_process_scans" name="Process Scans (and SIM-Stitch)" version="@TOOL_VERSION@+galaxy1">
0 62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	2 <description> - Read, filter and average MS scans</description>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	3 <macros>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	4 <import>macros.xml</import>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	5 </macros>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	6 <expand macro="requirements" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	7 <command detect_errors="exit_code">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	8 <![CDATA[
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	9 #if $data.input[0].is_of_type("zip")
1 deafa30d6570 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 680116d0cf6a6d7246cba655452dea43269aeba4" computational-metabolomics parents: 0 diff changeset	10 dimspy unzip
deafa30d6570 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 680116d0cf6a6d7246cba655452dea43269aeba4" computational-metabolomics parents: 0 diff changeset	11 --input $data.input[0]
deafa30d6570 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 680116d0cf6a6d7246cba655452dea43269aeba4" computational-metabolomics parents: 0 diff changeset	12 --output ./data
deafa30d6570 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 680116d0cf6a6d7246cba655452dea43269aeba4" computational-metabolomics parents: 0 diff changeset	13 &&
0 62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	14 dimspy process-scans
1 deafa30d6570 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 680116d0cf6a6d7246cba655452dea43269aeba4" computational-metabolomics parents: 0 diff changeset	15 --input ./data
0 62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	16 #else
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	17 #for $fn in $data.input
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	18 ln -s '$fn' '$fn.name'
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	19 &&
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	20 #end for
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	21 dimspy process-scans
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	22 --input .
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	23 #end if
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	24 --output '$hdf5_file_out'
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	25 #if $filelist
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	26 --filelist '$filelist'
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	27 #end if
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	28 --function-noise $function_noise
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	29 --snr-threshold $snr_threshold
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	30 --ppm $mults.ppm
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	31 --min_scans $mults.min_scans
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	32 #if float($mults.min_fraction) > 0.0
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	33 --min-fraction $mults.min_fraction
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	34 #else
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	35 --min-fraction 0.0
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	36 #end if
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	37 #if float($mults.rsd_threshold) > 0.0
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	38 --rsd-threshold $mults.rsd_threshold
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	39 #end if
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	40 #if $adv.skip_stitching
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	41 --skip-stitching
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	42 #end if
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	43 #if float($adv.ringing_threshold) > 0.0
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	44 --ringing-threshold $adv.ringing_threshold
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	45 #end if
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	46 #for $mzr in $adv.remove_mz_range
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	47 --remove-mz-range $mzr.start $mzr.end
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	48 #end for
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	49 #if $scan_events.filter == 'true'
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	50 #for $se in $scan_events.descriptions
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	51 #if $scan_events.incl_excl == 'include'
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	52 --include-scan-events $se.start $se.end $se.scan_type
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	53 #elif $scan_events.incl_excl == 'exclude'
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	54 --exclude-scan-events $se.start $se.end $se.scan_type
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	55 #end if
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	56 #end for
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	57 #end if
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	58 --report '$report'
2 bc099f2346a1 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448" computational-metabolomics parents: 1 diff changeset	59 --ncpu \${GALAXY_SLOTS:-1}
0 62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	60 &&
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	61 dimspy hdf5-pls-to-txt
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	62 --input '$hdf5_file_out'
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	63 --output .
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	64 --delimiter $delimiter
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	65 ]]>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	66 </command>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	67 <inputs>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	68 <conditional name="data">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	69 <param name="type" type="select" label="Select the MS data file type?">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	70 <option value="mzml" selected="true">*.mzML files</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	71 <option value="raw">*.raw files</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	72 </param>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	73 <when value="raw">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	74 <param name="license_agreement" type="boolean" label="Do you agree to the RawFileReader license terms?" help="*.raw files are read using the RawFileReader reading tool (Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved). To run this tool and process .raw files you must agree to the RawFileReader license terms. Read it at https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/tools/dimspy/RawFileReaderLicense.md. See generic help section of this tool for more details.">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	75 <validator type="expression" message="You must agree to the RawFileReader license terms to run this tool and process *.raw files.">True == value</validator>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	76 </param>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	77 <param name="input" argument="--source" type="data" format="thermo.raw" multiple="true" label="*.raw files" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	78 </when>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	79 <when value="mzml">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	80 <param name="input" argument="--source" type="data" format="zip,mzml" multiple="true" label="*.mzML files" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	81 </when>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	82 </conditional>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	83 <param name="filelist" argument="--filelist" type="data" format="tsv,tabular" optional="true" label="Filelist / Samplelist" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	84 <param name="function_noise" argument="--function-noise" type="select" label="Function to calculate the noise from each scan" help="">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	85 <option value="median" selected="true">median intensity</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	86 <option value="mean">mean intensity</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	87 <option value="mad">mad (mean absolute deviation) intensity</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	88 <option value="noise_packets">As shown in Xcalibur Qual Browser (Available for *.RAW files only)</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	89 </param>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	90 <param name="snr_threshold" argument="--snr-threshold" type="float" value="3.0" label="Signal-to-noise ratio threshold" help="" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	91 <conditional name="scan_events">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	92 <param name="filter" type="boolean" label="Filter specific windows or scan events?" help="(--include-scan-events / --exclude-scan-events)"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	93 <when value="true">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	94 <param name="incl_excl" type="select" label="Include / Exclude scan event(s)" >
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	95 <option value="exclude" selected="true">Exclude</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	96 <option value="include">Include</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	97 </param>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	98 <repeat name="descriptions" title="Description">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	99 <param name="start" type="float" value="0" label="Start m/z for scan event"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	100 <param name="end" type="float" value="0" label="End m/z for scan event">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	101 <validator type="expression" message="M/z value must be larger than 0.0">float(value) > 0.0</validator>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	102 </param>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	103 <param name="scan_type" type="select" label="Scan type">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	104 <option value="full" selected="true">Full scan</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	105 <option value="sim">SIM scan</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	106 </param>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	107 </repeat>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	108 </when>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	109 <when value="false">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	110 </when>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	111 </conditional>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	112 <section name="mults" title="Show options for multiple scans" expanded="True">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	113 <param name="min_scans" argument="--min_scans" type="integer" min="1" value="1" label="Minimum number of scans required for each m/z window or event" help="" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	114 <param name="ppm" argument="--ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation in consecutive scans in parts per million." />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	115 <param name="min_fraction" argument="--min-fraction" type="float" min="0.0" max="1.0" value="0.0" label="Minimum fraction (i.e. percentage) of scans a peak has to be present in." help="Select '0' to skip this step." />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	116 <param name="rsd_threshold" argument="--rsd-threshold" type="float" min="0.0" value="0.0" label="Relative standard deviation threshold" help="Select '0' to skip this step. Maximum tolerated relative standard deviation (RSD) of the peak intensities across scans." />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	117 </section>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	118 <section name="adv" title="Show advanced options" expanded="True">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	119 <param name="skip_stitching" argument="--skip-stitching" type="boolean" value="false" label="Skip SIM-Stitching?" help="When set to 'yes' it will skip the processing step where (SIM) windows are 'stitched' or 'joined' together. Set this option to 'yes' if you like to proces individual scan/SIM windows (events/ranges) without 'stitching' them."/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	120 <repeat name="remove_mz_range" title="Remove m/z range(s)?">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	121 <param name="start" type="float" value="0.0" label="Start m/z of removal range"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	122 <param name="end" type="float" value="0.0" label="End m/z of removal range">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	123 <validator type="expression" message="M/z value must be larger than 0.0">float(value) > 0.0</validator>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	124 </param>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	125 </repeat>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	126 <param name="ringing_threshold" argument="--ringing-threshold" type="float" value="0.0" min="0.0" max="1.0" label="Relative intensity threshold used to remove ringing artifacts" help="Select '0' to skip this filter." />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	127 </section>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	128 <param name="delimiter" argument="--delimiter" type="hidden" value="tab" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	129 </inputs>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	130 <outputs>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	131 <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peaklists (HDF5 file)" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	132 <data name="report" format="txt" label="${tool.name} on ${on_string}: Report" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	133 <collection name="peaklists_txt" type="list" label="${tool.name} on ${on_string}: Peaklists">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	134 <discover_datasets pattern="(?P<designation>.+)\.txt" format="tsv" directory="." visible="false" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	135 </collection>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	136 </outputs>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	137 <tests>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	138 <test>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	139 <conditional name="data">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	140 <param name="type" value="mzml"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	141 <param name="input" value="batch04_QC17_rep02_263.mzML,batch04_QC17_rep01_262.mzML,batch04_QC17_rep03_264.mzML" ftype="mzml" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	142 </conditional>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	143 <param name="filelist" value="filelist_mzml_QC17_triplicate.txt" ftype="tsv" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	144 <param name="function" value="median" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	145 <param name="snr_threshold" value="100.0" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	146 <conditional name="mults">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	147 <param name="ppm" value="2.0" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	148 <param name="min_scans" value="1" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	149 <param name="min_fraction" value="0.5" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	150 <param name="rsd_threshold" value="0" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	151 </conditional>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	152 <param name="delimiter" value="tab" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	153 <output name="hdf5_file_out" value="pls_scan5.h5" ftype="h5" compare="sim_size"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	154 <output name="report" value="report_pls_scan5.txt" ftype="txt"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	155 <output_collection name="peaklists_txt" type="list">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	156 <element name="batch04_QC17_rep01_262" file="batch04_QC17_rep01_262_scan5.txt" ftype="tsv"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	157 <element name="batch04_QC17_rep02_263" file="batch04_QC17_rep02_263_scan5.txt" ftype="tsv"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	158 <element name="batch04_QC17_rep03_264" file="batch04_QC17_rep03_264_scan5.txt" ftype="tsv"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	159 </output_collection>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	160 </test>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	161 <test>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	162 <conditional name="data">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	163 <param name="type" value="mzml"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	164 <param name="input" value="MTBLS79_mzml_triplicates.zip" ftype="zip"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	165 </conditional>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	166 <param name="filelist" value="filelist_mzml_triplicates.txt" ftype="tsv" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	167 <param name="function" value="median" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	168 <param name="snr_threshold" value="10.0" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	169 <conditional name="mults">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	170 <param name="ppm" value="2.0" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	171 <param name="min_scans" value="1" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	172 <param name="min_fraction" value="0.5" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	173 <param name="rsd_threshold" value="0" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	174 </conditional>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	175 <param name="delimiter" value="tab" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	176 <output name="hdf5_file_out" value="pls.h5" ftype="h5" compare="sim_size"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	177 <output name="report" value="report_pls_01.xt" ftype="txt"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	178 <output_collection name="peaklists_txt" type="list">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	179 <element name="batch04_QC17_rep01_262" file="batch04_QC17_rep01_262.txt" ftype="tsv"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	180 <element name="batch04_QC17_rep02_263" file="batch04_QC17_rep02_263.txt" ftype="tsv"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	181 <element name="batch04_QC17_rep03_264" file="batch04_QC17_rep03_264.txt" ftype="tsv"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	182 </output_collection>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	183 </test>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	184 <test>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	185 <conditional name="data">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	186 <param name="type" value="mzml"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	187 <param name="input" value="batch_04_QC18_mzml_triplicate.zip" ftype="zip"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	188 </conditional>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	189 <param name="function" value="median" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	190 <param name="snr_threshold" value="10.0" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	191 <conditional name="mults">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	192 <param name="ppm" value="2.0" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	193 <param name="min_scans" value="1" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	194 <param name="min_fraction" value="0.8" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	195 <param name="rsd_threshold" value="20.0" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	196 </conditional>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	197 <param name="delimiter" value="tab" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	198 <output name="hdf5_file_out" value="pls_QC18.h5" ftype="h5" compare="sim_size"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	199 <output name="report" value="report_pls_02.xt" ftype="txt"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	200 <output_collection name="peaklists_txt" type="list">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	201 <element name="batch04_QC18_rep01_280" file="batch04_QC18_rep01_280.txt" ftype="tsv"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	202 <element name="batch04_QC18_rep02_281" file="batch04_QC18_rep02_281.txt" ftype="tsv"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	203 <element name="batch04_QC18_rep03_282" file="batch04_QC18_rep03_282.txt" ftype="tsv"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	204 </output_collection>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	205 </test>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	206 </tests>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	207 <help>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	208
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	209
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	210 Process Scans (and SIM stitch)
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	211 ==============================
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	212
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	213 ..
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	214
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	215 ----------------
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	216
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	217 Description
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	218 -----------
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	219
1 deafa30d6570 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 680116d0cf6a6d7246cba655452dea43269aeba4" computational-metabolomics parents: 0 diff changeset	220 Standard DIMS processing workflow: Process Scans -> [Replicate Filter] -> Align Samples -> [Missing values sample filter] -> Blank Filter -> Sample Filter -> [Missing values sample filter] -> Pre-processing -> Statistics
0 62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	221
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	222 This tool is used to generate a single mass spectral peaklist for each of the data files defined in the ‘Filelist/Samplelist’. The tool extracts mass spectral peaks from a data file (in either .mzML or .RAW format) and then filters these in accordance with user-defined parameter settings. All peaks remaining after filtering are hierarchically clustered in one-dimension, during which pairs of peaks with similar m/z values are grouped together if the difference between their m/z values, when divided by the average of their m/z values and multiplied by 1 x 10\ :sup:`6` \, equates to less-than the user-defined ppm error tolerance.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	223
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	224 IMPORTANT: when using .mzML files generated using the Proteowizard tool, SIM-type scans will only be treated as spectra if the ‘simAsSpectra’ filter was set to true during the conversion process, e.g.:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	225
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	226 msconvert.exe example.raw --simAsSpectra --64 --zlib --filter "peakPicking true 1-”
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	227
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	228 -----------------
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	229
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	230
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	231 Parameters
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	232 ----------
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	233
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	234 **.mzml or .raw files** (REQUIRED) - use one of the following inputs:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	235
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	236 * Single or multiple .mzML or .raw file
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	237
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	238 * Data collection - use this option if .mzml or .raw files are contained within a Galaxy dataset collection. Dataset collections may be generated within the Galaxy environment.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	239
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	240 * Zip file from history - use this option if you have uploaded a \.zip directory containing \.mzML files (.raw files are not supported).
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	241
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	242
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	243 Filelist / Samplelist (HIGHLY RECOMMENDED) - a table containing filename and classLabel information for each experimental sample. These column headers MUST be included in the first row of the table.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	244
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	245 For a standard DIMS experiment, users are advised to also include the following additional columns in order to ensure their data remains compatible with future versions of the dimspy processing pipeline:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	246
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	247 * injectionOrder - integer values ranging from 1 to i, where i is the total number of independent infusions performed as part of a DIMS experiment. e.g. if a study included 20 samples, each of which was injected as four independent replicates, there would be at least 20 * 4 injections, so i = 80 and the range for injection order would be from 1 to 80 in steps of 1.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	248
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	249 * replicate - integer value from 1 to r, indicating the order in which technical replicates of each study sample were injected in to the mass spectrometer, e.g. if study samples were analysed in quadruplicate, r = 4 and integer values are accordingly 1, 2, 3, 4.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	250
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	251 * batch - integer value from 1 to b, where b corresponds to the total number of batches analysed under define analysis conditions, for any given experiment. e.g. : if 4 independent plates of polar extracts were analysed in the positive ionisation mode, then valid values for batch are 1, 2, 3 and 4.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	252
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	253 * NOTE: for DIMS experiments, “batch” is synonymous with plate, i.e. each independent plate analysed under a given analytical configuration may be considered an individual “batch”.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	254
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	255 This file:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	256
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	257 * must be uploaded to (or be accessible to) the active Galaxy history in order to allow for its selection in the Filelist / Samplelist drop-down menu. The file list / sample list may be created in .txt format, however, when imported in to the active Galaxy history, users must ensure to select ‘.tabular’ format.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	258
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	259 * may include additional columns, e.g. additional metadata relating to study samples. Ensure that columns names do not conflict with existing column names.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	260
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	261 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	262
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	263 @example_filelist@
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	264
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	265 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	266
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	267 Function to calculate the noise from each scan (REQUIRED; default = median) - toggle requiring selection of one option from the drop-down menu to indicate the preferred algorithm to apply for spectral noise calculation. The following options are available:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	268
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	269 * Median - the median of all peak intensities within a given file is used as the noise value. This simplistic approach to estimating noise may be suitable for spectra with many low abundant features, but it is generally not recommended for use when spectra contain relatively few low-abundant peaks e.g. MS2 spectra.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	270
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	271 * Mean - the unweighted mean average of all peak intensities within a given file is used as the noise value. This simplistic approach to estimating noise may be suitable for spectra with many low abundant features, but it is generally not recommended for use when spectra contain relatively few low-abundant peaks e.g. MS2 spectra.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	272
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	273 * Mean absolute deviation (MAD) - the noise value is set as the mean of the absolute differences between peak intensities and the mean peak intensity (calculated across all peak intensities within a given file).
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	274
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	275 * Xcalibur - the noise value is calculated using the proprietary algorithms contained in Thermo Fisher Scientific’s reader libdrary. This option should only be applied when you are processing .RAW files.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	276
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	277 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	278
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	279 Signal-to-noise ratio (SNR) threshold (REQUIRED; default = 3.0) - a numerical value from 0 upwards.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	280
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	281 Peaks with a signal-to-noise ratio (SNR) less-than or equal-to this value will be removed from the output peaklist. In the comprehensive peaklist output (.tsv-formatted), peaks with a SNR below the user-defined threshold will have a ‘0’ in the ‘snr-flag’ column, which indicates that they should be ignored in downstream processing procedures. Peaks with a SNR exceeding the user-defined cutoff will have a ‘1’ in the ‘snr-flag’ column.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	282
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	283 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	284
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	285 Filter specific scan windows or scan events? (OPTIONAL; default = No) - a boolean toggle where:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	286
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	287 * No - do not perform scan event filtering;
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	288
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	289 * Yes - filter specific scan events
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	290
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	291 * when selected, users must specify whether to 'Exclude' or 'Include' specific scan events. This can be useful if, for example, a user wishes to run the Process Scans tool on only a subset of scan types collected in each file. e.g. some SIM stitch acquisitions may be initiated with an initial 30 second stabilisation period, during which full-scan data are acquired. This full-scan data can be excluded from further consideration by using the ‘exclude’ toggle.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	292
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	293 * Included or excluded scan events must be fully defined by the user, else ALL scan events will be included. To do so:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	294 * Click the '+ Description' button and insert the start and stop m/z values for the scan event to be included/excluded..
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	295 * Select the 'scan type' to be filtered. Options are: 'Full scan' or 'SIM scan'
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	296 * Click '+ Description' to 'Exclude/Include' an additional scan event.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	297
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	298 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	299
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	300 Show options for multiple scans (OPTIONAL)
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	301
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	302 * Minimum number of scans required for each m/z window or event within a raw/mzML data file (default = 1) - A positive integer equal-to or greater-than 1 that specifies the number of times a given scan event must occur in a given file in order for this scan event to be included in downstream processing steps and in the output .tsv-formatted peaklist.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	303
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	304 * ppm error tolerance (default = 2.0) - A positive numerical value equal-to or greater-than zero. This option impacts the clustering of peaks extracted from an input file. If the mass-to-charge ratios of two peaks, when divided by the average of their mass-to-charge ratios and then multiplied by 1 × 106, is equal-to or less-than this user-defined value, then these peaks are clustered together as a single peak. Clustering is applied across all replicates of a given scan event type i.e. with a given input file, all peaks detected in the three replicates of a 50-400 m/z scan event would undergo assessment for the need for clustering.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	305
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	306 * Minimum fraction (i.e. percentage; default = 0, i.e. skip) of scans a peak has to be present in - A numerical value from 0 to 1 that specifies the minimum proportion of scans a given mass spectral peak must be detected in, in order for it to be kept in the output peaklist. Here, scans refers to replicates of the same scan event type, i.e. if set to 0.33, then a peak would need to be detected in at least 1 of the 3 replicates of a given scan event type. The ppm error specified by the user will significantly impact which peaks fulfil this criteria.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	307
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	308 * Relative standard deviation threshold (default = 0, i.e. skip) - A numerical value equal-to or greater-than 0. If greater than 0, then peaks whose intensity values have a percent relative standard deviation (otherwise termed the percent coefficient of variation) greater-than this value are excluded from the output peaklist.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	309
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	310 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	311
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	312 Show advanced options (OPTIONAL)
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	313
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	314 * Skip SIM-stitching (REQUIRED; default = No) - a boolean toggle where:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	315
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	316 * No - perform SIM stitching
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	317
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	318 * Yes - skip the processing step where (SIM) windows are 'stitched' or 'joined' together. Use this option if you would like to process individual scan/SIM windows (events/ranges) without 'stitching' them.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	319
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	320 * Remove m/z range(s) (OPTIONAL) - this option allows for specific regions of the output peak matrices to be deleted by the user - this option may be useful for removing sections of a spectrum known to correspond to system noise peaks.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	321
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	322 * Start m/z of removal range - a positive numerical value corresponding to the lowest m/z value in the spectral region to be removed.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	323
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	324 * End m/z of removal range - a positive numerical value corresponding to the highest m/z value in the spectral region to be removed (must be greater than the ‘start m/z of removal range’).
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	325
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	326 * Relative intensity threshold used to remove ringing artefacts (OPTIONAL) - Fourier transform-based mass spectra often contain peaks (ringing artefacts) around spectral features arising from detection of charged, gas-phase bio-molecules.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	327
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	328 * A positive numerical value indicating the required relative intensity a peak must exceed (with reference to the largest peak in a cluster of peaks) in order to be retained.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	329
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	330 ----------------------------------
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	331
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	332
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	333 Output file(s)
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	334 --------------
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	335
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	336 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	337
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	338 The Process scans (and SIM stitch) tool will output three file types:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	339
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	340 1) A HDF5 file containing the processed peaklists
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	341
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	342 2) A processed peaklist, presented in tabular format, for each study sample specified in the filelist/samplelist. Each row corresponds to a single peak. Where multiple peaks were grouped together during the hierarchical clustering process, each peaklist metric constitutes an average of the groups’ values. Metrics included in the peaklist are:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	343
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	344 @help_columns_peaklist@
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	345
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	346 @example_peaklist@
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	347
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	348 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	349
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	350 3) A tabular “report” file that details, for each scan event processed in each file:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	351
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	352 * Scan range of scan event
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	353
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	354 * Scan number of scan event
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	355
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	356 * Number of peaks detected in scan event
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	357
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	358 * Median RSD of peaks detected in each scan event type (only applied if number of scans for a given scan event is <![CDATA[ > ]]> 1
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	359
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	360 -----------------------------------
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	361
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	362 @github_developers_contributors@
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	363 @license@
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	364
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	365 RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved. Using this galaxy tool implies the acceptance of the RawFileReader `license terms`_.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	366
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	367 .. _`license terms`: https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/tools/dimspy/RawFileReaderLicense.md
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	368
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	369 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	370 </help>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	371
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	372 <expand macro="citations" />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	373
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	374 </tool>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	375

Mercurial > repos > computational-metabolomics > dimspy_process_scans

annotate process_scans.xml @ 2:bc099f2346a1 draft default tip