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comparison macros.xml @ 1:6635b68da948 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
author jjohnson
date Tue, 30 Jun 2020 11:42:28 -0400
parents 925fffecea81
children 114b44e35d30
comparison
equal deleted inserted replaced
0:925fffecea81 1:6635b68da948
28 <requirements> 28 <requirements>
29 <requirement type="package" version="@VERSION@">encyclopedia</requirement> 29 <requirement type="package" version="@VERSION@">encyclopedia</requirement>
30 <yield/> 30 <yield/>
31 </requirements> 31 </requirements>
32 </xml> 32 </xml>
33 <token name="@ENCYCLOPEDIA_WIKI@">
34 EncyclopeDIA_ is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries.
35
36 .. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home
37 </token>
33 <xml name="citations"> 38 <xml name="citations">
34 <citations> 39 <citations>
35 <citation type="doi">10.1038/s41467-018-07454-w</citation> 40 <citation type="doi">10.1038/s41467-018-07454-w</citation>
36 <citation type="doi">10.1038/s41467-020-15346-1</citation> 41 <citation type="doi">10.1038/s41467-020-15346-1</citation>
37 <yield /> 42 <citation type="doi">10.1074/mcp.P119.001913</citation>
43 <yield/>
38 </citations> 44 </citations>
39 </xml> 45 </xml>
40 <token name="@CMD_IMPORTS@"> 46 <token name="@CMD_IMPORTS@">
41 #import re 47 #import re
42 #def identifier_or_name($input1) 48 #def identifier_or_name($input1)
75 #set $l_name = None 81 #set $l_name = None
76 #set $t_name = None 82 #set $t_name = None
77 </token> 83 </token>
78 84
79 <xml name="scan_input"> 85 <xml name="scan_input">
80 <param argument="-i" type="data" format="imzml,mzml" label="Spectrum file, .mzml or .dia"/> 86 <param argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format">
87 <help>@MSCONVERT_RAW@</help>
88 </param>
81 </xml> 89 </xml>
82 <token name="@LINK_SCAN_INPUT@"><![CDATA[ 90 <token name="@LINK_SCAN_INPUT@"><![CDATA[
83 #set $i_name = $ln_name($i) 91 #set $i_name = $ln_name($i)
84 ln -s '$i' '$i_name' && 92 ln -s '$i' '$i_name' &&
85 ]]></token> 93 ]]></token>
86 <token name="@SCAN_INPUT@"> 94 <token name="@SCAN_INPUT@">
87 -i '$i_name' 95 -i '$i_name'
88 </token> 96 </token>
89 97
90 <xml name="scan_inputs"> 98 <xml name="scan_inputs">
91 <param argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum file, .mzml or .dia"/> 99 <param argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format">
100 <help>@MSCONVERT_RAW@</help>
101 </param>
92 </xml> 102 </xml>
93 <token name="@LINK_SCAN_INPUTS@"><![CDATA[ 103 <token name="@LINK_SCAN_INPUTS@"><![CDATA[
94 #set $inputs_dir = 'inputs' 104 #set $inputs_dir = 'inputs'
95 mkdir -p $inputs_dir && 105 mkdir -p $inputs_dir &&
96 #for $sf in $i 106 #for $sf in $i
101 <token name="@SCAN_INPUTS@"> 111 <token name="@SCAN_INPUTS@">
102 -i '$inputs_dir' 112 -i '$inputs_dir'
103 </token> 113 </token>
104 114
105 <xml name="fasta_input"> 115 <xml name="fasta_input">
106 <param argument="-f" type="data" format="fasta" label="Background protein fasta database"/> 116 <param argument="-f" type="data" format="fasta" label="Background proteome protein fasta database">
117 <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help>
118 </param>
107 </xml> 119 </xml>
108 <token name="@LINK_FASTA_INPUT@"><![CDATA[ 120 <token name="@LINK_FASTA_INPUT@"><![CDATA[
109 #set $f_name = $ln_name($f) 121 #set $f_name = $ln_name($f)
110 ln -s '$f' '$f_name' && 122 ln -s '$f' '$f_name' &&
111 ]]></token> 123 ]]></token>
112 <token name="@FASTA_INPUT@"> 124 <token name="@FASTA_INPUT@">
113 -f '$f_name' 125 -f '$f_name'
114 </token> 126 </token>
115 127
116 <xml name="target_fasta"> 128 <xml name="target_fasta">
117 <param argument="-t" type="data" format="fasta" label="target FASTA file" optional="true"/> 129 <param argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"/>
118 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/> 130 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/>
119 </xml> 131 </xml>
120 <token name="@LINK_TARGET_FASTA@"><![CDATA[ 132 <token name="@LINK_TARGET_FASTA@"><![CDATA[
121 #if $t 133 #if $t
122 #set $t_name = $ln_name($t) 134 #set $t_name = $ln_name($t)
130 -t '$t_name' 142 -t '$t_name'
131 -tp $tp 143 -tp $tp
132 #end if 144 #end if
133 </token> 145 </token>
134 146
135 <xml name="lib_input" token_optional="true" token_help=""> 147 <xml name="lib_input" token_optional="true" token_libhelp="">
136 <param argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB"> 148 <param argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB">
137 <help>@HELP@</help> 149 <help>@LIBHELP@</help>
138 </param> 150 </param>
139 </xml> 151 </xml>
140 <token name="@LINK_LIB_INPUT@"><![CDATA[ 152 <token name="@LINK_LIB_INPUT@"><![CDATA[
141 #if $l 153 #if $l
142 #set $l_name = $ln_name($l) 154 #set $l_name = $ln_name($l)
482 ## -beta $search.beta 494 ## -beta $search.beta
483 ## -addDecoysToBackground $search.addDecoysToBackground 495 ## -addDecoysToBackground $search.addDecoysToBackground
484 ## -dontRunDecoys $search.dontRunDecoys 496 ## -dontRunDecoys $search.dontRunDecoys
485 #end if 497 #end if
486 </token> 498 </token>
487 <!--
488 minNumOfQuantitativePeaks minQuantitativeIonNumber numberOfQuantitativePeaks numberOfReportedPeaksu
489 +acquisition (default: overlapping dia)
490 +addDecoysToBackground (default: false)
491 +alpha (default: 1.8)
492 +beta (default: 0.4)
493 +dontRunDecoys (default: false)
494 +enzyme (default: trypsin)
495 +filterPeaklists (default: false)
496 +fixed (default: C=57.0214635)
497 +foffset (default: 0)
498 =frag (default: YONLY)
499 +ftol (default: 10)
500 +ftolunits (default: ppm)
501 +maxCharge (default: 3)
502 +ftolunits (default: ppm)
503 +maxCharge (default: 3)
504 +maxLength (default: 100)
505 +maxMissedCleavage (default: 1)
506 +minCharge (default: 2)
507 +minEluteTime (default: 12)
508 +minIntensity (default: -1.0)
509 +minLength (default: 5)
510 +minNumOfQuantitativePeaks (default: 3)
511 +minQuantitativeIonNumber (default: 3)
512 +numberOfQuantitativePeaks (default: 5)
513 -numberOfReportedPeaks (default: 1)
514 -numberOfThreadsUsed (default: 12)
515 +percolatorProteinThreshol (default: 0.01)
516 +percolatorThreshold (default: 0.01)
517 +percolatorVersionNumber (default: 3)
518 +poffset (default: 0)
519 +precursorIsolationMargin (default: 0)
520 +precursorWindowSize (default: -1)
521 +ptol (default: 10)
522 +ptolunits (default: ppm)
523 -requireVariableMods (default: false)
524 -variable (default: -)
525 -->
526 <xml name="libexport"> 499 <xml name="libexport">
527 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/> 500 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/>
528 </xml> 501 </xml>
502 <token name="@MSCONVERT_CMD@"><![CDATA[
503 msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw
504 ]]>
505 </token>
506 <token name="@MSCONVERT_RAW@"><![CDATA[
507 mzML conversion from RAW requires special options: @MSCONVERT_CMD@
508 ]]>
509 </token>
510 <token name="@MSCONVERT_HELP@"><![CDATA[
511
512 The MSConvert command can be used to deconvolute DIA raw files. You need to use these options
513
514 ::
515
516 @MSCONVERT_CMD@
517
518 ]]>
519 </token>
529 </macros> 520 </macros>
530 <!--
531 e w t x l param
532 +:+:+:+:+ i
533 +:+:+:+:+ l
534 +:+:+:+:+ f
535
536 +:+:+:+:+ t
537 -:+:-:+:- tp
538 -:+:-:+:+ a
539
540 +:+:+:+:+ o
541
542 +:+:+:+:- acquisition
543 -:+:-:+:- addDecoysToBackground
544 -:+:-:+:- alpha
545 -:+:-:+:- beta
546 -:-:-:-:+ blib
547 -:+:-:+:- dontRunDecoys
548 +:+:+:+:- enzyme
549 +:-:+:-:- expectedPeakWidth
550 +:+:+:+:- filterPeaklists
551 +:+:+:+:+ fixed
552 +:+:+:+:+ foffset
553 +:+:+:+:- frag
554 +:+:+:+:+ ftol
555 +:+:+:+:+ ftolunits
556 +:-:+:-:- lftol
557 +:-:+:-:- lftolunits
558 +:-:-:-:- libexport
559 +:-:+:-:+ localizationModification
560 -:+:-:+:- maxCharge
561 -:+:-:+:- maxLength
562 -:+:-:+:- maxMissedCleavage
563 -:+:-:+:- minCharge
564 -:+:-:+:- minEluteTime
565 +:+:+:+:- minIntensity
566 -:+:-:+:- minLength
567 +:+:+:+:+ minNumOfQuantitativePeaks
568 +:+:+:+:+ minQuantitativeIonNumber
569 +:-:+:-:+ numberOfExtraDecoyLibrariesSearched
570 +:+:+:+:+ numberOfQuantitativePeaks
571 -:+:-:+:- numberOfReportedPeaks
572 -:+:-:+:- numberOfThreadsUsed
573 -:-:-:-:+ percolatorLocation
574 -:+:-:+:- percolatorProteinThreshol
575 +:-:+:-:+ percolatorProteinThreshold
576 +:+:+:+:+ percolatorThreshold
577 +:+:+:+:- percolatorVersionNumber
578 -:-:-:-:+ phospho
579 +:+:+:+:- poffset
580 +:+:+:+:- precursorIsolationMargin
581 +:+:+:+:- precursorWindowSize
582 +:+:+:+:- ptol
583 +:+:+:+:- ptolunits
584 -:+:-:+:- requireVariableMods
585 +:-:+:-:- rtWindowInMin
586 +:-:+:-:- scoringBreadthType
587 -:+:-:+:- variable
588 +:-:+:-:- verifyModificationIons
589 -->