encyclopedia: macros.xml annotate

annotate macros.xml @ 1:8f2555d3687f draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 7567c513925da467828c9f0dc1746a16b4adb062

author	galaxyp
date	Fri, 20 Sep 2019 11:01:22 -0400
parents	39618cb4669f
children

rev	line source
0 39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	1 <macros>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	2 <token name="@VERSION@">0.9.0</token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	3 <xml name="requirements">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	4 <requirements>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	5 <requirement type="package" version="@VERSION@">encyclopedia</requirement>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	6 <yield/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	7 </requirements>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	8 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	9 <xml name="citations">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	10 <citations>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	11 <yield />
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	12 </citations>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	13 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	14 <token name="@CMD_IMPORTS@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	15 #import re
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	16 #set $i_name = None
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	17 #set $f_name = None
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	18 #set $l_name = None
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	19 #set $t_name = None
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	20 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	21
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	22 <xml name="scan_input">
1 8f2555d3687f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 7567c513925da467828c9f0dc1746a16b4adb062 galaxyp parents: 0 diff changeset	23 <param argument="-i" type="data" format="imzml,mzml" label="Spectrum file, .mzml or .dia"/>
0 39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	24 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	25 <token name="@LINK_SCAN_INPUT@"><![CDATA[
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	26 #set $i_name = $i.display_name
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	27 ln -s '$i' '$i_name' &&
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	28 ]]></token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	29 <token name="@SCAN_INPUT@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	30 -i '$i_name'
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	31 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	32
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	33 <xml name="scan_inputs">
1 8f2555d3687f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 7567c513925da467828c9f0dc1746a16b4adb062 galaxyp parents: 0 diff changeset	34 <param argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum file, .mzml or .dia"/>
0 39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	35 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	36 <token name="@LINK_SCAN_INPUTS@"><![CDATA[
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	37 #set $inputs_dir = 'inputs'
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	38 mkdir -p $inputs_dir &&
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	39 #for $sf in $i
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	40 #set $i_name = $sf.display_name
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	41 ln -s '$sf' '${inputs_dir}/${i_name}' &&
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	42 #end for
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	43 ]]></token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	44 <token name="@SCAN_INPUTS@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	45 -i '$inputs_dir'
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	46 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	47
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	48 <xml name="fasta_input">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	49 <param argument="-f" type="data" format="fasta" label="Background protein fasta database"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	50 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	51 <token name="@LINK_FASTA_INPUT@"><![CDATA[
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	52 #set $f_name = $f.display_name
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	53 ln -s '$f' '$f_name' &&
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	54 ]]></token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	55 <token name="@FASTA_INPUT@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	56 -f '$f_name'
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	57 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	58
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	59 <xml name="target_fasta">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	60 <param argument="-t" type="data" format="fasta" label="target FASTA file" optional="true"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	61 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	62 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	63 <token name="@LINK_TARGET_FASTA@"><![CDATA[
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	64 #if $t
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	65 #set $t_name = $t.display_name
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	66 ln -s '$t' '$t_name' &&
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	67 #else
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	68 #set $t_name = None
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	69 #end if
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	70 ]]></token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	71 <token name="@TARGET_FASTA@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	72 #if $t_name
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	73 -t '$t_name'
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	74 -tp $tp
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	75 #end if
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	76 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	77
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	78 <xml name="lib_input">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	79 <param argument="-l" type="data" format="elib,dlib" label="Library: Chromatagram .ELIB or Spectrum .DLIB"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	80 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	81 <token name="@LINK_LIB_INPUT@"><![CDATA[
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	82 #set $l_name = $l.display_name
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	83 cp '$l' $l_name &&
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	84 ]]></token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	85 <token name="@LIB_INPUT@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	86 -l '$l_name'
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	87 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	88
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	89 <xml name="common_options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	90 <section name="acquisition" expanded="true" title="Acquisition Options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	91 <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	92 <param argument="-acquisition" type="select" label="Data Acquization Type">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	93 <option value="Non-Overlapping DIA">Non-Overlapping DIA</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	94 <option value="Overlapping DIA">Overlapping DIA</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	95 </param>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	96 <param argument="-enzyme" type="select" label="Digestion Enzyme">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	97 <option value="Trypsin">Trypsin</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	98 <option value="Trypsin/p">Trypsin/p</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	99 <option value="Lys-C">Lys-C</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	100 <option value="Lys-N">Lys-N</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	101 <option value="Arg-C">Arg-C</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	102 <option value="Glu-C">Glu-C</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	103 <option value="Chymotrypsin">Chymotrypsin</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	104 <option value="Pepsin A">Pepsin A</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	105 <option value="Elastase">Elastase</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	106 <option value="Thermolysin">Thermolysin</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	107 <option value="No Enzyme">No Enzyme</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	108 </param>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	109 <param argument="-frag" type="select" label="Fragmentation">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	110 <option value="CID">CID/HCD (B/Y)</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	111 <option value="HCD">HCD (Y-Only)</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	112 <option value="ETD">ETD (C/Z/Z+1)</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	113 </param>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	114 </section>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	115 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	116 <token name="@COMMON_OPTIONS@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	117 -numberOfExtraDecoyLibrariesSearched $acquisition.numberOfExtraDecoyLibrariesSearched
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	118 -acquisition '$acquisition.acquisition'
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	119 -enzyme '$acquisition.enzyme'
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	120 -frag '$acquisition.frag'
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	121 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	122
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	123 <xml name="mass_tolerance">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	124 <section name="tolerance" expanded="true" title="Tolerance Options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	125 <conditional name="precursor_tolerance">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	126 <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	127 <option value="PPM">PPM</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	128 <option value="AMU">AMU</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	129 <option value="Resolution">Resolution</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	130 </param>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	131 <when value="PPM">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	132 <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	133 </when>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	134 <when value="AMU">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	135 <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	136 </when>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	137 <when value="Resolution">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	138 <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	139 </when>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	140 </conditional>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	141 <conditional name="fragment_tolerance">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	142 <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	143 <option value="PPM">PPM</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	144 <option value="AMU">AMU</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	145 <option value="Resolution">Resolution</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	146 </param>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	147 <when value="PPM">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	148 <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	149 </when>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	150 <when value="AMU">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	151 <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	152 </when>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	153 <when value="Resolution">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	154 <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	155 </when>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	156 </conditional>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	157 <yield/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	158 </section>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	159 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	160 <token name="@MASS_TOLERANCE@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	161 -ptolunits $tolerance.precursor_tolerance.ptolunits
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	162 -ptol $tolerance.precursor_tolerance.ptol
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	163 -ftolunits $tolerance.fragment_tolerance.ftolunits
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	164 -ftol $tolerance.fragment_tolerance.ftol
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	165 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	166
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	167 <xml name="mass_library_tolerance">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	168 <expand macro="mass_tolerance">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	169 <conditional name="library_tolerance">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	170 <param argument="-ltolunits" type="select" label="Library Mass Tolerance">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	171 <option value="PPM">PPM</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	172 <option value="AMU">AMU</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	173 <option value="Resolution">Resolution</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	174 </param>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	175 <when value="PPM">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	176 <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	177 </when>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	178 <when value="AMU">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	179 <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	180 </when>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	181 <when value="Resolution">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	182 <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	183 </when>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	184 </conditional>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	185 </expand>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	186 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	187 <token name="@MASS_LIBRARY_TOLERANCE@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	188 @MASS_TOLERANCE@
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	189 -ltolunits $tolerance.library_tolerance.ltolunits
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	190 -ltol $tolerance.library_tolerance.ltol
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	191 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	192
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	193 <xml name="percolator_options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	194 <section name="percolator" expanded="false" title="Pecolator Options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	195 <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	196 <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	197 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	198 </section>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	199 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	200 <token name="@PERCOLATOR_OPTIONS@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	201 #if str($percolator.percolatorVersionNumber)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	202 -percolatorVersionNumber $percolator.percolatorVersionNumber
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	203 #end if
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	204 #if str($percolator.percolatorProteinThreshold)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	205 -percolatorProteinThreshold $percolator.percolatorProteinThreshold
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	206 #end if
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	207 #if str($percolator.percolatorThreshold)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	208 -percolatorThreshold $percolator.percolatorThreshold
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	209 #end if
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	210 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	211
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	212 <xml name="peak_options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	213 <section name="peak" expanded="false" title="Peak Options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	214 <param argument="-numberOfQuantitativePeaks" type="integer" value="5" min="1" max="100" label="Number of Quantitative Peaks"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	215 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="0" max="100" label="Minimum Number of Quantitative Peaks"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	216 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="0" max="100" label="Minimum Number of Quantitative Ions"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	217 <param argument="-minIntensity" type="float" value="-1.0" label="minIntensity"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	218 <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" label="Expected Peak Width"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	219 <param argument="-filterPeaklists" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Filter Peak Lists"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	220 </section>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	221 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	222 <token name="@PEAK_OPTIONS@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	223 #if str($peak.numberOfQuantitativePeaks)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	224 -numberOfQuantitativePeaks $peak.numberOfQuantitativePeaks
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	225 #end if
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	226 #if str($peak.minNumOfQuantitativePeaks)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	227 -minNumOfQuantitativePeaks $peak.minNumOfQuantitativePeaks
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	228 #end if
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	229 #if str($peak.minQuantitativeIonNumber)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	230 -minQuantitativeIonNumber $peak.minQuantitativeIonNumber
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	231 #end if
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	232 #if str($peak.minIntensity)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	233 -minIntensity $peak.minIntensity
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	234 #end if
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	235 #if str($peak.expectedPeakWidth)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	236 -expectedPeakWidth $peak.expectedPeakWidth
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	237 #end if
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	238 -filterPeaklists $peak.filterPeaklists
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	239 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	240
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	241 <xml name="window_options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	242 <section name="window" expanded="false" title="Window Options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	243 <param argument="-foffset" type="integer" value="0" label="fragmentOffsetPPM"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	244 <param argument="-poffset" type="integer" value="0" label="Precursor Offset PPM" help="-poffset"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	245 <param argument="-precursorIsolationMargin" type="integer" value="0" label="precursorIsolationMargin"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	246 <param argument="-precursorWindowSize" type="integer" value="-1" label="precursorWindowSize"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	247 <param argument="-rtWindowInMin" type="float" value="-1.0" label="rtWindowInMin"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	248 <param argument="-scoringBreadthType" type="select" label="scoringBreadthType">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	249 <option value="window">Across entire window</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	250 <option value="recal20">Recalibrated (20% gradient)</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	251 <option value="recal">Recalibrated (peak width only)</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	252 <option value="uncal20">Uncalibrated (20% gradient)</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	253 <option value="uncal">Uncalibrated (peak width only)</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	254 </param>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	255 </section>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	256 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	257 <token name="@WINDOW_OPTIONS@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	258 -foffset $window.foffset
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	259 -poffset $window.poffset
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	260 -precursorIsolationMargin $window.precursorIsolationMargin
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	261 -precursorWindowSize $window.precursorWindowSize
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	262 -rtWindowInMin $window.rtWindowInMin
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	263 -scoringBreadthType $window.scoringBreadthType
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	264 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	265
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	266 <xml name="modification_options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	267 <section name="modifications" expanded="false" title="Modification Options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	268 <param argument="-fixed" type="select" label="Fixed Modification">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	269 <option value="C=57.0214635">C=57.0214635</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	270 </param>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	271 <!--
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	272 <param argument="-localizationModification" type="select" optional="true" label="localizationModification">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	273 </param>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	274 -->
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	275 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	276 </section>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	277 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	278 <token name="@MODIFICATION_OPTIONS@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	279 -verifyModificationIons $modifications.verifyModificationIons
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	280 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	281
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	282 <xml name="search_options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	283 <section name="search" expanded="false" title="Search Options">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	284 <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	285 <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	286 <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	287 <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	288 <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	289 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	290 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	291 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	292 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	293 <param argument="-alpha" type="float" value="1.8" min="0.0" max="5.0" label="alpha"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	294 <param argument="-beta" type="float" value="0.4" min="0.0" max="5.0" label="beta"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	295 <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	296 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	297 </section>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	298 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	299 <token name="@SEARCH_OPTIONS@">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	300 -minCharge $search.minCharge
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	301 -maxCharge $search.maxCharge
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	302 -minLength $search.minLength
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	303 -maxLength $search.maxLength
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	304 -minEluteTime $search.minEluteTime
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	305 -maxMissedCleavage $search.maxMissedCleavage
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	306 -minQuantitativeIonNumber $search.minQuantitativeIonNumber
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	307 -minNumOfQuantitativePeaks $search.minNumOfQuantitativePeaks
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	308 -numberOfQuantitativePeaks $search.numberOfQuantitativePeaks
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	309 -alpha $search.alpha
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	310 -beta $search.beta
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	311 -addDecoysToBackground $search.addDecoysToBackground
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	312 -dontRunDecoys $search.dontRunDecoys
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	313 </token>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	314 minNumOfQuantitativePeaks minQuantitativeIonNumber numberOfQuantitativePeaks numberOfReportedPeaksu
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	315 <!--
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	316 +acquisition (default: overlapping dia)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	317 +addDecoysToBackground (default: false)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	318 +alpha (default: 1.8)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	319 +beta (default: 0.4)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	320 +dontRunDecoys (default: false)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	321 +enzyme (default: trypsin)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	322 +filterPeaklists (default: false)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	323 +fixed (default: C=57.0214635)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	324 +foffset (default: 0)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	325 =frag (default: YONLY)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	326 +ftol (default: 10)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	327 +ftolunits (default: ppm)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	328 +maxCharge (default: 3)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	329 +maxLength (default: 100)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	330 +maxMissedCleavage (default: 1)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	331 +minCharge (default: 2)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	332 +minEluteTime (default: 12)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	333 +minIntensity (default: -1.0)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	334 +minLength (default: 5)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	335 +minNumOfQuantitativePeaks (default: 3)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	336 +minQuantitativeIonNumber (default: 3)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	337 +numberOfQuantitativePeaks (default: 5)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	338 -numberOfReportedPeaks (default: 1)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	339 -numberOfThreadsUsed (default: 12)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	340 +percolatorProteinThreshol (default: 0.01)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	341 +percolatorThreshold (default: 0.01)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	342 +percolatorVersionNumber (default: 3)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	343 +poffset (default: 0)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	344 +precursorIsolationMargin (default: 0)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	345 +precursorWindowSize (default: -1)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	346 +ptol (default: 10)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	347 +ptolunits (default: ppm)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	348 -requireVariableMods (default: false)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	349 -variable (default: -)
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	350 -->
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	351 <xml name="libexport">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	352 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="true" label="align between files"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	353 </xml>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	354 </macros>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	355 <!--
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	356 e w t x l param
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	357 +:+:+:+:+ i
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	358 +:+:+:+:+ l
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	359 +:+:+:+:+ f
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	360
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	361 +:+:+:+:+ t
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	362 -:+:-:+:- tp
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	363 -:+:-:+:+ a
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	364
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	365 +:+:+:+:+ o
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	366
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	367 +:+:+:+:- acquisition
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	368 -:+:-:+:- addDecoysToBackground
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	369 -:+:-:+:- alpha
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	370 -:+:-:+:- beta
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	371 -:-:-:-:+ blib
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	372 -:+:-:+:- dontRunDecoys
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	373 +:+:+:+:- enzyme
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	374 +:-:+:-:- expectedPeakWidth
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	375 +:+:+:+:- filterPeaklists
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	376 +:+:+:+:+ fixed
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	377 +:+:+:+:+ foffset
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	378 +:+:+:+:- frag
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	379 +:+:+:+:+ ftol
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	380 +:+:+:+:+ ftolunits
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	381 +:-:+:-:- lftol
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	382 +:-:+:-:- lftolunits
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	383 +:-:-:-:- libexport
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	384 +:-:+:-:+ localizationModification
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	385 -:+:-:+:- maxCharge
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	386 -:+:-:+:- maxLength
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	387 -:+:-:+:- maxMissedCleavage
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	388 -:+:-:+:- minCharge
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	389 -:+:-:+:- minEluteTime
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	390 +:+:+:+:- minIntensity
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	391 -:+:-:+:- minLength
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	392 +:+:+:+:+ minNumOfQuantitativePeaks
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	393 +:+:+:+:+ minQuantitativeIonNumber
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	394 +:-:+:-:+ numberOfExtraDecoyLibrariesSearched
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	395 +:+:+:+:+ numberOfQuantitativePeaks
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	396 -:+:-:+:- numberOfReportedPeaks
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	397 -:+:-:+:- numberOfThreadsUsed
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	398 -:-:-:-:+ percolatorLocation
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	399 -:+:-:+:- percolatorProteinThreshol
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	400 +:-:+:-:+ percolatorProteinThreshold
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	401 +:+:+:+:+ percolatorThreshold
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	402 +:+:+:+:- percolatorVersionNumber
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	403 -:-:-:-:+ phospho
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	404 +:+:+:+:- poffset
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	405 +:+:+:+:- precursorIsolationMargin
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	406 +:+:+:+:- precursorWindowSize
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	407 +:+:+:+:- ptol
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	408 +:+:+:+:- ptolunits
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	409 -:+:-:+:- requireVariableMods
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	410 +:-:+:-:- rtWindowInMin
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	411 +:-:+:-:- scoringBreadthType
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	412 -:+:-:+:- variable
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	413 +:-:+:-:- verifyModificationIons
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f galaxyp parents: diff changeset	414 -->

Mercurial > repos > galaxyp > encyclopedia

annotate macros.xml @ 1:8f2555d3687f draft default tip