spectrast: macros.xml annotate

annotate macros.xml @ 4:c9bfe6adb7cd draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty

author	jjohnson
date	Wed, 25 Jul 2018 14:41:20 -0400
parents	7f02fc51bddf
children

rev	line source
0 4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	1 <macros>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	2 <token name="@VERSION@">5.0.0</token>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	3 <xml name="requirements">
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	4 <requirements>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	5 <requirement type="package" version="5.0.0">tpp</requirement>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	6 <yield/>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	7 </requirements>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	8 </xml>
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	9 <token name="@LIBRARY_CREATE_OPTIONS@">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	10 outputFileName = ${output.extra_files_path}/library.splib
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	11 #if str($library_create.removeDecoyProteins) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	12 removeDecoyProteins = $library_create.removeDecoyProteins
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	13 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	14 #if str($library_create.useProbTable) != 'None':
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	15 useProbTable = $library_create.useProbTable
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	16 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	17 #if str($library_create.useProteinList) != 'None':
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	18 useProteinList = $library_create.useProteinList
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	19 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	20 #if str($library_create.printMRMTable) in ['true']:
c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	21 printMRMTable = DEFAULT
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	22 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	23 #if str($library_create.writeMgfFile) in ['true','false']:
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	24 writeMgfFile = $library_create.writeMgfFile
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	25 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	26 ## #if str($library_create.writeDtaFiles) in ['true','false']:
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	27 ## writeDtaFiles = $library_create.writeDtaFiles
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	28 ## #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	29 #if str($library_create.writePAIdent) in ['true','false']:
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	30 writePAIdent = $library_create.writePAIdent
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	31 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	32 </token>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	33 <xml name="library_create_outputs">
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	34 <data name="library_pai" format="tabular" label="library.PAIdent" from_work_dir="outdir/library.PAIdent">
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	35 <filter>library_create['writePAIdent'] == 'true'</filter>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	36 </data>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	37 <data name="library_mrm" format="tabular" label="library.mrm" from_work_dir="outdir/library.mrm">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	38 <filter>library_create['printMRMTable'] == 'true'</filter>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	39 </data>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	40 <data name="library_mgf" format="mgf" label="library.mgf" from_work_dir="outdir/library.mgf">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	41 <filter>library_create['writeMgfFile'] == 'true'</filter>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	42 </data>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	43 <!--
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	44 <data name="library_mgf" format="dta" label="library.mgf" from_work_dir="outdir/library.mrm">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	45 <filter>library_create['writeDtaFiles'] == 'true'</filter>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	46 </data>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	47 -->
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	48 </xml>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	49 <xml name="library_create_options">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	50 <section name="library_create" expanded="false" title="Library Create Options">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	51 <param name="removeDecoyProteins" type="text" value="" optional="true" label="removeDecoyProteins Default: true" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	52 <help> Remove spectra of decoys, for which proteins have names starting with this prefix. Also remove decoy proteins from Protein field for peptides mapped to both target and decoy sequences.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	53 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	54 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	55
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	56 <param name="useProbTable" type="data" format="tabular" optional="true" label="Peptide ion probability table">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	57 <help><![CDATA[
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	58 Only those peptide ions included in the table will be imported, and their probability adjusted optionally.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	59 A probability table is a text file with one peptide ion in the format AC[160]DEFGHIK/2 per line. If a probability is supplied following the peptide ion separated by a tab, it will be used to replace the original probability of that library entry.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	60 ]]></help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	61 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	62 <param name="useProteinList" type="data" format="tabular" optional="true" label="Protein list">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	63 <help><![CDATA[
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	64 Only those peptide ions associated with proteins in the list will be imported.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	65 A protein list is a text file with one protein identifier per line.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	66 If a number X is supplied following the protein separated by a tab,
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	67 then at most X peptide ions associated with that protein will be imported.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	68 Peptides with more replicates are favored.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	69 ]]></help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	70 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	71 <param name="printMRMTable" type="select" optional="true" label="printMRMTable Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	72 <help> Write library in binary format, which enables quicker search.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	73 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	74 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	75 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	76 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	77 <param name="writeMgfFile" type="select" optional="true" label="writeMgfFile Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	78 <help> Write all library spectra as one .mgf file
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	79 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	80 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	81 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	82 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	83 <!--
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	84 <param name="writeDtaFiles" type="select" optional="true" label="writeDtaFiles Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	85 <help> Write library in binary format, which enables quicker search.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	86 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	87 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	88 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	89 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	90 -->
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	91 <param name="writePAIdent" type="select" optional="true" label="writePAIdent Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	92 <help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	93 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	94 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	95 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	96 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	97 </section>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	98 </xml>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	99 <token name="@LIBRARY_IMPORT_OPTIONS@">
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	100 #if str($library_import.minimumProbabilityToInclude) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	101 minimumProbabilityToInclude = $library_import.minimumProbabilityToInclude
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	102 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	103 #if str($library_import.maximumFDRToInclude) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	104 maximumFDRToInclude = $library_import.maximumFDRToInclude
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	105 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	106 #if str($library_import.setFragmentation) != 'None':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	107 setFragmentation = $library_import.setFragmentation
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	108 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	109 #if str($library_import.setDeamidatedNXST) != 'None':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	110 setDeamidatedNXST = $library_import.setDeamidatedNXST
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	111 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	112 #if str($library_import.addMzXMLFileToDatasetName) != 'None':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	113 addMzXMLFileToDatasetName = $library_import.addMzXMLFileToDatasetName
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	114 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	115 #if str($library_import.centroidPeaks) != 'None':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	116 centroidPeaks = $library_import.centroidPeaks
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	117 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	118 #if str($library_import.rawSpectraNoiseThreshold) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	119 rawSpectraNoiseThreshold = $library_import.rawSpectraNoiseThreshold
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	120 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	121 #if str($library_import.rawSpectraMaxDynamicRange) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	122 rawSpectraMaxDynamicRange = $library_import.rawSpectraMaxDynamicRange
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	123 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	124 #if str($library_import.minimumNumAAToInclude) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	125 minimumNumAAToInclude = $library_import.minimumNumAAToInclude
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	126 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	127 #if str($library_import.minimumNumPeaksToInclude) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	128 minimumNumPeaksToInclude = $library_import.minimumNumPeaksToInclude
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	129 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	130 #if str($library_import.skipRawAnnotation) != 'None':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	131 skipRawAnnotation = $library_import.skipRawAnnotation
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	132 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	133 #if str($library_import.minimumDeltaCnToInclude) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	134 minimumDeltaCnToInclude = $library_import.minimumDeltaCnToInclude
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	135 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	136 #if str($library_import.maximumMassDiffToInclude) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	137 maximumMassDiffToInclude = $library_import.maximumMassDiffToInclude
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	138 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	139 #if str($library_import.bracketSpectra) != 'None':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	140 bracketSpectra = $library_import.bracketSpectra
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	141 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	142 #if str($library_import.mergeBracket) != 'None':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	143 mergeBracket = $library_import.mergeBracket
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	144 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	145 #if str($library_import.normalizeRTWithLandmarks) != 'None':
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	146 normalizeRTWithLandmarks = $library_import.normalizeRTWithLandmarks
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	147 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	148 #if str($library_import.normalizeRTLinearRegression) != 'None':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	149 normalizeRTLinearRegression = $library_import.normalizeRTLinearRegression
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	150 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	151 </token>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	152 <xml name="library_import_options">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	153 <section name="library_import" expanded="false" title="Library Import Options">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	154 <param name="minimumProbabilityToInclude" type="float" value="" min="0.0" max="1.0" optional="true"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	155 label="minimumProbabilityToInclude"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	156 help="Include all spectra identified with probability no less than this in the library. Default is 0.9"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	157 <param name="maximumFDRToInclude" type="float" value="" min="0.0" optional="true"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	158 label="maximumFDRToInclude for pepXML import"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	159 help="(Only for pepXML import) Include spectra with global FDR no greater than this in the library. Default is 999.0"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	160 <param name="setFragmentation" type="select" optional="true" label="Set the fragmentation type of all spectra, overriding existing information" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	161 <help>Default is off (determined from the data files).
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	162 Examples: CID, ETD, CID-QTOF, HCD. The latter two are treated as high-mass accuracy spectra.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	163 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	164 <option value="ETD">ETD spectra</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	165 <option value="CID-QTOF">CID-QTOF spectra</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	166 <option value="HCD">HCD spectra</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	167 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	168 <param name="setDeamidatedNXST" type="select" optional="true" label="setDeamidatedNXST Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	169 <help> Set all asparagines (N) in the motif NX(S/T) as deamidated (N[115]),
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	170 and all asparagines not in the motif NX(S/T) as unmodified.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	171 Use for glycocaptured peptides.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	172 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	173 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	174 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	175 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	176 <param name="addMzXMLFileToDatasetName" type="select" optional="true" label="addMzXMLFileToDatasetName Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	177 <help> Add the originating mzXML file name to the dataset identifier.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	178 Good for keeping track of the MS run in which the peptide is observed.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	179 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	180 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	181 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	182 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	183 <param name="centroidPeaks" type="select" optional="true" label="centroidPeaks Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	184 <help> Centroid peaks as raw spectra are imported.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	185 Designed mostly for Q-TOF spectra in profile mode.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	186 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	187 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	188 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	189 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	190 <param name="rawSpectraNoiseThreshold" type="float" value="" min="0.0" optional="true"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	191 label="rawSpectraNoiseThreshold"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	192 help="Absolute noise filter. Remove noise peaks with intensity below this in imported spectra. Default is 0.0"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	193 <param name="rawSpectraMaxDynamicRange" type="float" value="" min="1.0" optional="true"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	194 label="rawSpectraMaxDynamicRange"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	195 help="Relative noise filter. Filter out noise peaks with intensity below 1/range of that of the highest peak. Default is 100000.0"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	196 <param name="minimumNumAAToInclude" type="integer" value="" optional="true" min="1"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	197 label="minimumNumAAToInclude"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	198 help="Exclude spectra of peptide IDs shorter than this number of amino acids. Default is 6"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	199 <param name="minimumNumPeaksToInclude" type="integer" value="" optional="true" min="1"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	200 label="minimumNumPeaksToInclude"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	201 help="Exclude spectra with fewer than this number of peaks. Default is 10"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	202 <param name="skipRawAnnotation" type="select" optional="true" label="skipRawAnnotation Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	203 <help> Skip the annotation of raw spectra as they are imported.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	204 Annotation is quite slow and might be impractical if the number of imported spectra is enormous.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	205 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	206 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	207 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	208 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	209 <param name="minimumDeltaCnToInclude" type="float" value="" min="0.0" optional="true"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	210 label="minimumDeltaCnToInclude"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	211 help="(Only for pepXML import) Exclude spectra with deltaCn smaller than this. Useful for excluding spectra with indiscriminate modification sites. Default is 0.0"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	212 <param name="maximumMassDiffToInclude" type="float" value="" min="0.0" optional="true"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	213 label="maximumMassDiffToInclude"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	214 help="(Only for pepXML import) Exclude spectra with precursor mass difference (absolute value) greater than this numbers of Daltons. Default is 9999.0"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	215 <param name="bracketSpectra" type="select" optional="true" label="bracketSpectra Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	216 <help> (Only for pepXML import)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	217 Bracket import: for each confident ID, also search neighboring scans for repeated scans to import.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	218 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	219 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	220 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	221 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	222 <param name="mergeBracket" type="select" optional="true" label="mergeBracket Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	223 <help> (Only for pepXML import)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	224 Merge bracketed spectra: merge repeated scans of a bracket into one consensus spectrum for import.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	225 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	226 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	227 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	228 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	229 <param name="normalizeRTWithLandmarks" type="data" format="tabular" optional="true"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	230 label="normalizeRTWithLandmarks Use landmark peptides to normalize retention times to iRTs."
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	231 help="A TAB-delimited table with two columns: peptide sequence and iRT" />
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	232 <param name="normalizeRTLinearRegression" type="select" optional="true" label="normalizeRTLinearRegression Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	233 <help> Regress the real RTs of landmark peptides (i.e. assume they form a straight line).
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	234 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	235 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	236 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	237 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	238 </section>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	239 </xml>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	240
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	241 <token name="@LIBRARY_MANIPULATION_OPTIONS@">
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	242 #if str($library_manipulation.filterCriteria) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	243 filterCriteria = $library_manipulation.filterCriteria
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	244 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	245 #if str($library_manipulation.combineAction) != 'None':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	246 combineAction = $library_manipulation.combineAction
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	247 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	248 #if $library_manipulation.build.buildAction != 'NONE':
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	249 buildAction = $library_manipulation.build.buildAction
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	250 #if $library_manipulation.build.buildAction in ['BEST_REPLICATE','CONSENSUS']:
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	251 #if str($library_manipulation.build.build_bc_action.minimumNumReplicates) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	252 minimumNumReplicates = $library_manipulation.build.build_bc_action.minimumNumReplicates
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	253 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	254 #if str($library_manipulation.build.build_bc_action.removeDissimilarReplicates) in ['true','false']:
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	255 removeDissimilarReplicates = $library_manipulation.build.build_bc_action.removeDissimilarReplicates
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	256 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	257 #if str($library_manipulation.build.build_bc_action.peakQuorum) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	258 peakQuorum = $library_manipulation.build.build_bc_action.peakQuorum
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	259 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	260 #if str($library_manipulation.build.build_bc_action.maximumNumPeaksUsed) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	261 maximumNumPeaksUsed = $library_manipulation.build.build_bc_action.maximumNumPeaksUsed
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	262 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	263 #if str($library_manipulation.build.build_bc_action.maximumNumReplicates) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	264 maximumNumReplicates = $library_manipulation.build.build_bc_action.maximumNumReplicates
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	265 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	266 #if str($library_manipulation.build.build_bc_action.maximumNumPeaksKept) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	267 maximumNumPeaksKept = $library_manipulation.build.build_bc_action.maximumNumPeaksKept
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	268 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	269 #if str($library_manipulation.build.build_bc_action.replicateWeight) != 'None':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	270 replicateWeight = $library_manipulation.build.build_bc_action.replicateWeight
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	271 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	272 #if str($library_manipulation.build.build_bc_action.recordRawSpectra) in ['true','false']:
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	273 recordRawSpectra = $library_manipulation.build.build_bc_action.recordRawSpectra
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	274 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	275 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	276 #if $library_manipulation.build.buildAction == 'DECOY':
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	277 #if str($library_manipulation.build.build_d_action.decoyConcatenate) in ['true','false']:
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	278 decoyConcatenate = $library_manipulation.build.build_d_action.decoyConcatenate
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	279 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	280 #if str($library_manipulation.build.build_d_action.decoySizeRatio) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	281 decoySizeRatio = $library_manipulation.build.build_d_action.decoySizeRatio
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	282 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	283 #if str($library_manipulation.build.build_d_action.decoyPrecursorSwap) in ['true','false']:
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	284 decoyPrecursorSwap = $library_manipulation.build.build_d_action.decoyPrecursorSwap
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	285 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	286 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	287 #if $library_manipulation.build.buildAction == 'USER_SPECIFIED_MODS':
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	288 #if str($library_manipulation.build.build_m_action.allowableModTokens) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	289 allowableModTokens = $library_manipulation.build.build_m_action.allowableModTokens
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	290 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	291 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	292 #if $library_manipulation.build.buildAction == 'QUALITY_FILTER':
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	293 #if str($library_manipulation.build.build_q_action.minimumNumReplicates) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	294 minimumNumReplicates = $library_manipulation.build.build_q_action.minimumNumReplicates
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	295 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	296 #if str($library_manipulation.build.build_q_action.qualityLevelRemove) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	297 qualityLevelRemove = $library_manipulation.build.build_q_action.qualityLevelRemove
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	298 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	299 #if str($library_manipulation.build.build_q_action.qualityLevelMark) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	300 qualityLevelMark = $library_manipulation.build.build_q_action.qualityLevelMark
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	301 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	302 #if str($library_manipulation.build.build_q_action.qualityPenalizeSingletons) in ['true','false']:
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	303 qualityPenalizeSingletons = $library_manipulation.build.build_q_action.qualityPenalizeSingletons
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	304 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	305 #if str($library_manipulation.build.build_q_action.qualityImmuneProbThreshold) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	306 qualityImmuneProbThreshold = $library_manipulation.build.build_q_action.qualityImmuneProbThreshold
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	307 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	308 #if str($library_manipulation.build.build_q_action.qualityImmuneMultipleEngines) in ['true','false']:
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	309 qualityImmuneMultipleEngines = $library_manipulation.build.build_q_action.qualityImmuneMultipleEngines
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	310 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	311 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	312 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	313 #if str($library_manipulation.reduceSpectra) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	314 reduceSpectra = $library_manipulation.reduceSpectra
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	315 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	316 #if str($library_manipulation.reannotatePeaks) in ['true','false']:
c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	317 reannotatePeaks = $library_manipulation.reannotatePeaks
c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	318 #end if
c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	319 #if str($library_manipulation.minimumNumPeaksToInclude) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	320 minimumNumPeaksToInclude = $library_manipulation.minimumNumPeaksToInclude
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	321 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	322 #if str($library_manipulation.minimumMRMQ3MZ) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	323 minimumMRMQ3MZ = $library_manipulation.minimumMRMQ3MZ
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	324 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	325 #if str($library_manipulation.maximumMRMQ3MZ) != '':
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	326 maximumMRMQ3MZ = $library_manipulation.maximumMRMQ3MZ
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	327 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	328 #if $library_manipulation.db.refresh == 'yes':
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	329 refreshDatabase = $library_manipulation.db.refreshDatabase
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	330 #if str($library_manipulation.db.refreshDeleteUnmapped) in ['true','false']:
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	331 refreshDeleteUnmapped = $library_manipulation.db.refreshDeleteUnmapped
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	332 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	333 #if str($library_manipulation.db.refreshDeleteMultimapped) in ['true','false']:
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	334 refreshDeleteMultimapped = $library_manipulation.db.refreshDeleteMultimapped
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	335 #end if
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	336 #if str($library_manipulation.db.refreshTrypticOnly) in ['true','false']:
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	337 refreshTrypticOnly = $library_manipulation.db.refreshTrypticOnly
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	338 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	339 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	340 </token>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	341 <xml name="library_build_bc_opts">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	342 <section name="build_bc_action" expanded="false" title="Consensus/Best-Replicate Library Creation Build Options">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	343 <param name="minimumNumReplicates" type="integer" value="" optional="true" min="1"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	344 label="minimumNumReplicates"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	345 help="Minimum number of replicates required for each library entry. Peptide ions with fewer than this numer of replicates will be excluded from library when creating consensus library. Default is 1"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	346 <param name="removeDissimilarReplicates" type="select" optional="true" label="removeDissimilarReplicates Default: true" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	347 <help> Remove dissimilar replicates before creating consensus spectrum.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	348 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	349 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	350 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	351 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	352 <param name="peakQuorum" type="float" value="" min="0.0" max="1.0" optional="true"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	353 label="peakQuorum"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	354 help="Specify peak quorum: the fraction of all replicates required to contain a certain peak. Peaks not present in enough replicates will be deleted. Default is 0.6"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	355 <param name="maximumNumPeaksUsed" type="integer" value="" optional="true" min="1"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	356 label="maximumNumPeaksUsed"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	357 help="Maximum number of peaks in each replicate to be considered in creating consensus. Only the most intense number of peaks by intensity will be considered. Default is 300"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	358 <param name="maximumNumReplicates" type="integer" value="" optional="true" min="1"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	359 label="maximumNumReplicates"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	360 help="Maximum number of replicates used to build consensus spectrum. Default is 100"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	361 <param name="maximumNumPeaksKept" type="integer" value="" optional="true" min="1"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	362 label="maximumNumPeaksKept"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	363 help="De-noise single spectra by keeping only this number of the most intense peaks. Will not affect consensus spectra of more than one replicate. Default is 150"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	364 <param name="replicateWeight" type="select" optional="true" label="replicateWeight Default: signal-to-noise ratio" >
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	365 <help> Select the type of score to weigh and rank the replicates.
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	366 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	367 <option value="NONE">NONE</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	368 <option value="SN">Use a measure of signal-to-noise ratio as the weight.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	369 <option value="XCORR">Use a function of the SEQUEST xcorr score as the weight.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	370 <option value="PROB">Use a function of the PeptideProphet probability as the weight.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	371 <option value="INTP">Use the sqrt of precursor intensity</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	372 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	373 <param name="recordRawSpectra" type="select" optional="true" label="recordRawSpectra Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	374 <help> Record all raw spectra (in the format file.scan.scan) used in build the consensus in the Comment line.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	375 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	376 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	377 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	378 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	379 </section>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	380 </xml>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	381 <xml name="library_build_d_opts">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	382 <section name="build_d_action" expanded="false" title="Decoy Library Creation Build Options">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	383 <param name="decoyConcatenate" type="select" optional="true" label="decoyConcatenate Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	384 <help> Concatenate real and decoy libraries. Default is false: library consisting of only decoy spectra is created.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	385 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	386 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	387 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	388 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	389 <param name="decoySizeRatio" type="integer" value="" optional="true" min="1"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	390 label="decoySizeRatio"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	391 help="Specify the (decoy / real) size ratio. Default is 1"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	392 <param name="decoyPrecursorSwap" type="select" optional="true" label="decoyPrecursorSwap Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	393 <help> Use a modified form of the precursor swap method for generating decoys.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	394 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	395 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	396 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	397 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	398 </section>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	399 </xml>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	400 <xml name="library_build_m_opts">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	401 <section name="build_m_action" expanded="false" title="Usr Mods Library Creation Build Options">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	402 <param name="allowableModTokens" type="text" value="" optional="true" label="allowableModTokens">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	403 <help><![CDATA[
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	404 Specify the set(s) of modifications allowed in semi-empirical spectrum generation.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	405 ]]></help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	406 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	407 </section>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	408 </xml>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	409 <xml name="quality_level_opts">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	410 <option value="0">0: No filter.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	411 <option value="1">1: Remove/mark impure spectra.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	412 <option value="2">2: Also remove/mark spectra with a spectrally similar counterpart in the library that is better.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	413 <option value="3">3: Also remove/mark inquorate entries (defined with minimumNumReplicates) that share no peptide sub-sequences with any other entries in the library. </option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	414 <option value="4">4: Also remove/mark all singleton entries.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	415 <option value="5">5: Also remove/mark all inquorate entries (defined with minimumNumReplicates).</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	416 </xml>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	417 <xml name="library_build_q_opts">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	418 <section name="build_q_action" expanded="false" title="Quality Filter Library Creation Build Options">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	419 <param name="minimumNumReplicates" type="integer" value="" optional="true" min="1"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	420 label="minimumNumReplicates"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	421 help="Replicate quorum. Its value affects behavior of quality filter. Default is 1"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	422 <param name="qualityLevelRemove" type="select" optional="true" label="qualityLevelRemove Default: 2" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	423 <help> Specify the removal stringency of the quality filter
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	424 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	425 <expand macro="quality_level_opts"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	426 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	427 <param name="qualityLevelMark" type="select" optional="true" label="qualityLevelMark Default: 5" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	428 <help> Specify the removal stringency of the quality filter
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	429 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	430 <expand macro="quality_level_opts"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	431 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	432 <param name="qualityPenalizeSingletons" type="select" optional="true" label="qualityPenalizeSingletons Default: true" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	433 <help> Apply stricter thresholds to singleton spectra during quality filters.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	434 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	435 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	436 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	437 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	438 <param name="qualityImmuneProbThreshold" type="float" value="" min="0.0" max="1.0" optional="true"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	439 label="qualityImmuneProbThreshold"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	440 help="Specify a probability above which library spectra are immune to quality filters. Default is 0.999"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	441 <param name="qualityImmuneMultipleEngines" type="select" optional="true" label="qualityImmuneMultipleEngines Default: true" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	442 <help> Make spectra identified by multiple sequence search engines immune to quality filters.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	443 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	444 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	445 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	446 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	447 </section>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	448 </xml>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	449 <xml name="library_manipulation_options">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	450 <section name="library_manipulation" expanded="false" title="Library Manipulation Options">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	451 <!-- filterCriteria -->
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	452
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	453 <param name="filterCriteria" type="text" value="" optional="true" label="filterCriteria">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	454 <help><![CDATA[
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	455 Filter library by criteria. Keep only those entries satisfying the predicate.
4 c9bfe6adb7cd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty jjohnson parents: 3 diff changeset	456 The predicate should in the form "<attr> <op> <value>".
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	457 <attr> can refer to any of the fields and any comment entries.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	458 <op> can be ==, !=, <, >, <=, >=, =~ and !~.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	459 Multiple predicates can be separated by either & (AND logic) or \| (OR logic), but not both.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	460 ]]></help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	461 <validator type="regex" message=""><![CDATA[^\S+ (==\|!=\|<\|>\|<=\|>=\|=~\|!~) \S+(( & \S+ (==\|!=\|<\|>\|<=\|>=\|=~\|!~) \S+)\|( [\|] \S+ (==\|!=\|<\|>\|<=\|>=\|=~\|!~) \S+ ))*$]]></validator>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	462 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	463 <param name="combineAction" type="select" optional="true" label="combineAction Default: Union" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	464 <help> How to combine peptides from multiple files
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	465 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	466 <option value="UNION">Union (default). Include all the peptide ions in all the files.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	467 <option value="INTERSECT">Intersection. Only include peptide ions that are present in all the files.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	468 <option value="SUBTRACT">Subtraction. Only include peptide ions in the first file that are not present in any of the other files.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	469 <option value="SUBTRACT_HOMOLOGS">Subtraction of homologs. Only include peptide ions in the first file that do not have any homologs with similar m/z in any of the other files.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	470 <option value="APPEND">Appending. Each peptide ion is added from only one library: the first one in the command line that contains that peptide ion. </option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	471 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	472 <conditional name="build">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	473 <param name="buildAction" type="select" label="buildAction" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	474 <help> How to built representative spectra instead of including all.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	475 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	476 <option value="NONE" selected="true">Default: no build action - all spectra will be included as is.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	477 <option value="BEST_REPLICATE">Best replicate. Pick the best replicate of each peptide ion.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	478 <option value="CONSENSUS">Consensus. Create the consensus spectrum of all replicate spectra of each peptide ion.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	479 <option value="QUALITY_FILTER">Quality filter. Apply quality filters to library.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	480 <option value="DECOY">Decoy. Generate decoy spectra.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	481 <option value="SORT_BY_NREPS">Sort by descending number of replicates (tie-breaking by probability).</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	482 <option value="USER_SPECIFIED_MODS">User-specified modifications. Generate semi-empirical spectra. (allowableModTokens required)</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	483 <option value="SIMILARITY_CLUSTERING">Semi-empirical. Generate semi-empirical spectra.</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	484 <option value="SEMI_EMPIRICAL_SPLIB">Clustering by spectral similarity. </option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	485 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	486 <when value="NONE"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	487 <when value="BEST_REPLICATE">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	488 <expand macro="library_build_bc_opts"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	489 </when>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	490 <when value="CONSENSUS">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	491 <expand macro="library_build_bc_opts"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	492 </when>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	493 <when value="QUALITY_FILTER">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	494 <expand macro="library_build_q_opts"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	495 </when>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	496 <when value="DECOY">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	497 <expand macro="library_build_d_opts"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	498 </when>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	499 <when value="SORT_BY_NREPS"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	500 <when value="USER_SPECIFIED_MODS">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	501 <expand macro="library_build_m_opts"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	502 </when>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	503 <when value="SIMILARITY_CLUSTERING"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	504 <when value="SEMI_EMPIRICAL_SPLIB"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	505 </conditional>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	506 <param name="reduceSpectra" type="integer" value="" optional="true" min="0"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	507 label="reduceSpectra"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	508 help="Produce reduced spectra of at most this number of peaks, based on rules prioritizing desirable SRM transitions. Default is 0 (keep entire spectrum)"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	509 <param name="reannotatePeaks" type="select" optional="true" label="reannotatePeaks Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	510 <help> Re-annotate peaks.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	511 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	512 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	513 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	514 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	515 <param name="minimumNumPeaksToInclude" type="integer" value="" optional="true" min="1"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	516 label="minimumNumPeaksToInclude"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	517 help="Exclude spectra with fewer than this number of peaks. Default is 10"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	518 <param name="minimumMRMQ3MZ" type="integer" value="" optional="true" min="1"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	519 label="minimumMRMQ3MZ"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	520 help="Specify the lower m/z limit for Q3 in SRM table generation. Default is 200."/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	521 <param name="maximumMRMQ3MZ" type="integer" value="" optional="true" min="1"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	522 label="maximumMRMQ3MZ"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	523 help="Specify the upper m/z limit for Q3 in SRM table generation. Default is 1400."/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	524 <conditional name="db">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	525 <param name="refresh" type="select" label="Refresh protein mappings against the FASTA database">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	526 <option value="no">No</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	527 <option value="yes">Yes</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	528 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	529 <when value="no"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	530 <when value="yes">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	531 <param name="refreshDatabase" type="data" format="fasta" label="Protein FASTA datadase"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	532 <param name="refreshDeleteUnmapped" type="select" optional="true" label="refreshDeleteUnmapped Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	533 <help> Delete entries whose peptide sequences do not map to any protein during refreshing.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	534 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	535 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	536 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	537 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	538 <param name="refreshDeleteMultimapped" type="select" optional="true" label="refreshDeleteMultimapped Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	539 <help> Delete entries whose peptide sequences map to multiple proteins during refreshing.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	540 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	541 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	542 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	543 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	544 <param name="refreshTrypticOnly" type="select" optional="true" label="refreshTrypticOnly Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	545 <help> Only map peptide to protein when the peptide is tryptic in that protein.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	546 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	547 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	548 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	549 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	550 </when>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	551 </conditional>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	552 </section>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	553 </xml>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	554 <token name="@LIBRARY_UNIDENTIFIED_OPTIONS@">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	555 #if $library_unidentified.unidentifiedClusterIndividualRun is not None:
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	556 unidentifiedClusterIndividualRun = $library_unidentified.unidentifiedClusterIndividualRun
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	557 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	558 #if $library_unidentified.unidentifiedClusterMinimumDot is not None:
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	559 unidentifiedClusterMinimumDot = $library_unidentified.unidentifiedClusterMinimumDot
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	560 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	561 #if $library_unidentified.unidentifiedRemoveSinglyCharged is not None:
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	562 unidentifiedRemoveSinglyCharged = $library_unidentified.unidentifiedRemoveSinglyCharged
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	563 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	564 #if $library_unidentified.unidentifiedMinimumNumPeaksToInclude is not None:
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	565 unidentifiedMinimumNumPeaksToInclude = $library_unidentified.unidentifiedMinimumNumPeaksToInclude
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	566 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	567 #if $library_unidentified.unidentifiedSingletonXreaThreshold is not None:
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	568 unidentifiedSingletonXreaThreshold = $library_unidentified.unidentifiedSingletonXreaThreshold
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	569 #end if
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	570 </token>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	571 <xml name="library_unidentified_options">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	572 <section name="library_unidentified" expanded="false" title="Library Clustering Unidentified Options">
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	573 <param name="unidentifiedClusterIndividualRun" type="select" optional="true" label="unidentifiedClusterIndividualRun Default: false" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	574 <help> Merge neighboring spectra in each run as they are imported from data (mz(X)ML) files.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	575 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	576 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	577 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	578 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	579 <param name="unidentifiedClusterMinimumDot" type="float" value="" min="0.0" max="1.0" optional="true"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	580 label="unidentifiedClusterMinimumDot"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	581 help="Specify minimum dot products for two spectra to be clustered. Default is 0.7"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	582
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	583 <param name="unidentifiedRemoveSinglyCharged" type="select" optional="true" label="unidentifiedRemoveSinglyCharged Default: true" >
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	584 <help> Remove spectra that appear to be from singly charged precursors.
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	585 </help>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	586 <option value="false">false</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	587 <option value="true">true</option>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	588 </param>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	589 <param name="unidentifiedMinimumNumPeaksToInclude" type="integer" value="" optional="true" min="1"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	590 label="unidentifiedMinimumNumPeaksToInclude"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	591 help="Remove spectra that have fewer than this number of peaks. Default is 35"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	592 <param name="unidentifiedSingletonXreaThreshold" type="float" value="" min="0.0" max="1.0" optional="true"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	593 label="unidentifiedSingletonXreaThreshold"
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	594 help="Apply an Xrea (quality measure) filter to singleton spectra after clustering. Only those with Xrea at least this theshold are kept. Default is 0.6"/>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	595 </section>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	596 </xml>
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 0 diff changeset	597
0 4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	598 <xml name="citations">
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	599 <citations>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	600 <citation type="doi">10.1002/pmic.200600625</citation>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	601 <yield />
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	602 </citations>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	603 </xml>
4e23dcad9087 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty jjohnson parents: diff changeset	604 </macros>

Mercurial > repos > jjohnson > spectrast

annotate macros.xml @ 4:c9bfe6adb7cd draft