Mercurial > repos > jjohnson > encyclopedia_quantify

annotate macros.xml @ 4:bd937e4efa04 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
author jjohnson
date Wed, 19 Aug 2020 08:38:25 -0400
parents aa52f0eadc85
children 30f6b9c88ceb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
1 <macros>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
2 <token name="@VERSION@">0.9.5</token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
3 <xml name="requirements">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
4 <requirements>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
5 <requirement type="package" version="@VERSION@">encyclopedia</requirement>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
6 <yield/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
7 </requirements>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
8 </xml>
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
9
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
10 <token name="@ENCYCLOPEDIA_WIKI@">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
11 EncyclopeDIA_ is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries.
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
12
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
13 .. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
14 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
15 <xml name="citations">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
16 <citations>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
17 <citation type="doi">10.1038/s41467-018-07454-w</citation>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
18 <citation type="doi">10.1038/s41467-020-15346-1</citation>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
19 <citation type="doi">10.1074/mcp.P119.001913</citation>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
20 <yield/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
21 </citations>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
22 </xml>
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
23
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
24 <token name="@CMD_IMPORTS@">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
25 #import re
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
26 #def identifier_or_name($input1)
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
27 #if hasattr($input1, 'element_identifier')
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
28 #return $input1.element_identifier
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
29 #else
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
30 #return $input1.name
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
31 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
32 #end def
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
33 #def clean($name1)
3
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 2
diff changeset
34 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
35 #return $name_clean
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
36 #end def
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
37 #def ln_name($ds)
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
38 #set $ext = ''
3
aa52f0eadc85 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
jjohnson
parents: 2
diff changeset
39 #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
40 #set $ext = ".mzML"
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
41 #else if $ds.is_of_type('elib')
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
42 #set $ext = ".elib"
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
43 #else if $ds.is_of_type('dlib')
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
44 #set $ext = ".dlib"
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
45 #else if $ds.is_of_type('blib')
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
46 #set $ext = ".blib"
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
47 #else if $ds.is_of_type('fasta')
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
48 #set $ext = ".fasta"
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
49 #else if $ds.is_of_type('fasta.gz')
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
50 #set $ext = ".fasta.gz"
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
51 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
52 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
53 #return $name
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
54 #end def
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
55 #set $i_name = None
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
56 #set $f_name = None
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
57 #set $l_name = None
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
58 #set $t_name = None
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
59 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
60
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
61 <xml name="scan_input">
4
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
62 <param name="scan_input" argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format">
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
63 <help>@MSCONVERT_RAW@</help>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
64 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
65 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
66 <token name="@LINK_SCAN_INPUT@"><![CDATA[
4
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
67 #set $i_name = $ln_name($scan_input)
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
68 ln -s '$scan_input' '$i_name' &&
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
69 ]]></token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
70 <token name="@SCAN_INPUT@">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
71 -i '$i_name'
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
72 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
73
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
74 <xml name="scan_inputs">
4
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
75 <param name="scan_inputs" argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format">
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
76 <help>@MSCONVERT_RAW@</help>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
77 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
78 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
79 <token name="@LINK_SCAN_INPUTS@"><![CDATA[
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
80 #set $inputs_dir = 'inputs'
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
81 mkdir -p $inputs_dir &&
4
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
82 #for $sf in $scan_inputs
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
83 #set $i_name = $ln_name($sf)
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
84 ln -s '$sf' '${inputs_dir}/${i_name}' &&
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
85 #end for
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
86 ]]></token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
87 <token name="@SCAN_INPUTS@">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
88 -i '$inputs_dir'
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
89 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
90
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
91 <xml name="fasta_input">
4
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
92 <param name="fasta" argument="-f" type="data" format="fasta" label="Background proteome protein fasta database">
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
93 <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
94 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
95 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
96 <token name="@LINK_FASTA_INPUT@"><![CDATA[
4
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
97 #set $f_name = $ln_name($fasta)
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
98 ln -s '$fasta' '$f_name' &&
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
99 ]]></token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
100 <token name="@FASTA_INPUT@">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
101 -f '$f_name'
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
102 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
103
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
104 <xml name="target_fasta">
4
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
105 <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"/>
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
106 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
107 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
108 <token name="@LINK_TARGET_FASTA@"><![CDATA[
4
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
109 #if $target_fasta
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
110 #set $t_name = $ln_name($target_fasta)
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
111 ln -s '$target_fasta' '$t_name' &&
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
112 #else
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
113 #set $t_name = None
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
114 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
115 ]]></token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
116 <token name="@TARGET_FASTA@">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
117 #if $t_name
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
118 -t '$t_name'
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
119 -tp $tp
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
120 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
121 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
122
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
123 <xml name="lib_input" token_optional="true" token_libhelp="">
4
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
124 <param name="library" argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB">
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
125 <help>@LIBHELP@</help>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
126 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
127 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
128 <token name="@LINK_LIB_INPUT@"><![CDATA[
4
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
129 #if $library
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
130 #set $l_name = $ln_name($library)
bd937e4efa04 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
jjohnson
parents: 3
diff changeset
131 cp '$library' $l_name &&
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
132 #else
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
133 #set $l_name = None
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
134 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
135 ]]></token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
136 <token name="@LIB_INPUT@">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
137 #if $l_name
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
138 -l '$l_name'
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
139 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
140 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
141
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
142 <xml name="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="false"
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
143 token_cid_selected="false" token_hcd_selected="false">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
144 <conditional name="acquisition">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
145 <param name="set_acquisition" type="select" label="Set Acquisition Options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
146 <option value="no">No - use default options</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
147 <option value="yes">Yes</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
148 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
149 <when value="no"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
150 <when value="yes">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
151 <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
152 <param argument="-acquisition" type="select" optional="true" label="Data Acquization Type">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
153 <option value="Overlapping DIA" selected="@OVERLAPPING_SELECTED@">Overlapping DIA</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
154 <option value="Non-Overlapping DIA" selected="@NONOVERLAPPING_SELECTED@">Non-Overlapping DIA</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
155 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
156 <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
157 <option value="Trypsin">Trypsin</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
158 <option value="Trypsin/p">Trypsin/p</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
159 <option value="Lys-C">Lys-C</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
160 <option value="Lys-N">Lys-N</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
161 <option value="Arg-C">Arg-C</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
162 <option value="Glu-C">Glu-C</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
163 <option value="Chymotrypsin">Chymotrypsin</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
164 <option value="Pepsin A">Pepsin A</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
165 <option value="Elastase">Elastase</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
166 <option value="Thermolysin">Thermolysin</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
167 <option value="No Enzyme">No Enzyme</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
168 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
169 <param argument="-frag" type="select" optional="true" label="Fragmentation">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
170 <option value="CID" selected="@CID_SELECTED@">CID/HCD (B/Y)</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
171 <option value="HCD" selected="@HCD_SELECTED@">HCD (Y-Only)</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
172 <option value="ETD">ETD (C/Z/Z+1)</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
173 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
174 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
175 </conditional>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
176 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
177 <xml name="encyclopedia_common_options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
178 <expand macro="common_options" token_overlapping_selected="true" token_nonoverlapping_selected="false"
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
179 token_cid_selected="true" token_hcd_selected="false"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
180 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
181 <xml name="walnut_common_options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
182 <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true"
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
183 token_cid_selected="false" token_hcd_selected="true"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
184 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
185 <token name="@COMMON_OPTIONS@">
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
186 #if $options.acquisition.set_acquisition == 'yes'
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
187 -numberOfExtraDecoyLibrariesSearched $options.acquisition.numberOfExtraDecoyLibrariesSearched
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
188 #if $options.acquisition.acquisition
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
189 -acquisition '$options.acquisition.acquisition'
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
190 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
191 #if $options.acquisition.enzyme:
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
192 -enzyme '$options.acquisition.enzyme'
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
193 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
194 #if $options.acquisition.frag:
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
195 -frag '$options.acquisition.frag'
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
196 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
197 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
198 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
199
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
200 <xml name="mass_tolerance">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
201 <conditional name="tolerance">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
202 <param name="set_tolerance" type="select" label="Set Tolerance Options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
203 <option value="no">No - use default options</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
204 <option value="yes">Yes</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
205 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
206 <when value="no"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
207 <when value="yes">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
208 <conditional name="precursor_tolerance">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
209 <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
210 <option value="PPM">PPM</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
211 <option value="AMU">AMU</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
212 <option value="Resolution">Resolution</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
213 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
214 <when value="PPM">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
215 <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
216 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
217 <when value="AMU">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
218 <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
219 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
220 <when value="Resolution">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
221 <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
222 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
223 </conditional>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
224 <conditional name="fragment_tolerance">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
225 <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
226 <option value="PPM">PPM</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
227 <option value="AMU">AMU</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
228 <option value="Resolution">Resolution</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
229 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
230 <when value="PPM">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
231 <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
232 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
233 <when value="AMU">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
234 <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
235 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
236 <when value="Resolution">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
237 <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
238 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
239 </conditional>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
240 <yield/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
241 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
242 </conditional>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
243 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
244 <token name="@MASS_TOLERANCE@">
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
245 #if $options.tolerance.set_tolerance == 'yes'
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
246 -ptolunits $options.tolerance.precursor_tolerance.ptolunits
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
247 -ptol $options.tolerance.precursor_tolerance.ptol
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
248 -ftolunits $options.tolerance.fragment_tolerance.ftolunits
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
249 -ftol $options.tolerance.fragment_tolerance.ftol
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
250 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
251 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
252
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
253 <xml name="mass_library_tolerance">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
254 <expand macro="mass_tolerance">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
255 <conditional name="library_tolerance">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
256 <param argument="-ltolunits" type="select" label="Library Mass Tolerance">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
257 <option value="defaults">Use defaults</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
258 <option value="PPM">PPM</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
259 <option value="AMU">AMU</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
260 <option value="Resolution">Resolution</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
261 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
262 <when value="defaults"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
263 <when value="PPM">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
264 <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
265 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
266 <when value="AMU">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
267 <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
268 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
269 <when value="Resolution">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
270 <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
271 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
272 </conditional>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
273 </expand>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
274 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
275 <token name="@MASS_LIBRARY_TOLERANCE@">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
276 @MASS_TOLERANCE@
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
277 #if $options.tolerance.set_tolerance == 'yes' and $options.tolerance.library_tolerance.ltolunits != 'defaults'
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
278 -ltolunits $options.tolerance.library_tolerance.ltolunits
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
279 -ltol $options.tolerance.library_tolerance.ltol
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
280 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
281 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
282
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
283 <xml name="percolator_options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
284 <conditional name="percolator">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
285 <param name="set_percolator" type="select" label="Set Percolator Options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
286 <option value="no">No - use default options</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
287 <option value="yes">Yes</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
288 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
289 <when value="no"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
290 <when value="yes">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
291 <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
292 <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
293 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
294 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
295 </conditional>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
296 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
297 <token name="@PERCOLATOR_OPTIONS@">
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
298 #if $options.percolator.set_percolator == 'yes'
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
299 #if str($options.percolator.percolatorVersionNumber)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
300 -percolatorVersionNumber $options.percolator.percolatorVersionNumber
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
301 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
302 #if str($options.percolator.percolatorProteinThreshold)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
303 -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
304 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
305 #if str($options.percolator.percolatorThreshold)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
306 -percolatorThreshold $options.percolator.percolatorThreshold
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
307 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
308 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
309 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
310
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
311 <xml name="peak_options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
312 <conditional name="peak">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
313 <param name="set_peak" type="select" label="Set Peak Options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
314 <option value="no">No - use default options</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
315 <option value="yes">Yes</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
316 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
317 <when value="no"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
318 <when value="yes">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
319 <param argument="-numberOfQuantitativePeaks" type="integer" value="" min="1" max="100" optional="true" label="Number of Quantitative Peaks" help="(default 5)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
320 <param argument="-minNumOfQuantitativePeaks" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Peaks" help="(default 3)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
321 <param argument="-minQuantitativeIonNumber" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Ions" help="(default 3)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
322 <param argument="-minIntensity" type="float" value="-1.0" optional="true" label="minIntensity"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
323 <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" optional="true" label="Expected Peak Width" help="(default 5)"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
324 <param argument="-filterPeaklists" type="select" optional="true" label="Filter Peak Lists">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
325 <option value="false">No</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
326 <option value="true">Yes</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
327 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
328 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
329 </conditional>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
330 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
331 <token name="@PEAK_OPTIONS@">
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
332 #if $options.peak.set_peak == 'yes'
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
333 #if str($options.peak.numberOfQuantitativePeaks)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
334 -numberOfQuantitativePeaks $options.peak.numberOfQuantitativePeaks
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
335 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
336 #if str($options.peak.minNumOfQuantitativePeaks)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
337 -minNumOfQuantitativePeaks $options.peak.minNumOfQuantitativePeaks
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
338 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
339 #if str($options.peak.minQuantitativeIonNumber)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
340 -minQuantitativeIonNumber $options.peak.minQuantitativeIonNumber
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
341 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
342 #if str($options.peak.minIntensity)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
343 -minIntensity $options.peak.minIntensity
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
344 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
345 #if str($options.peak.expectedPeakWidth)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
346 -expectedPeakWidth $options.peak.expectedPeakWidth
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
347 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
348 #if $options.peak.filterPeaklists
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
349 -filterPeaklists $options.peak.filterPeaklists
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
350 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
351 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
352 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
353
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
354 <xml name="window_options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
355 <conditional name="window">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
356 <param name="set_window" type="select" label="Set Window Options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
357 <option value="no">No - use default options</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
358 <option value="yes">Yes</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
359 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
360 <when value="no"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
361 <when value="yes">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
362 <param argument="-foffset" type="integer" value="" optional="true" label="fragmentOffsetPPM"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
363 <param argument="-poffset" type="integer" value="" optional="true" label="Precursor Offset PPM" help="-poffset"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
364 <param argument="-precursorIsolationMargin" type="integer" value="" optional="true" label="precursorIsolationMargin"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
365 <param argument="-precursorWindowSize" type="integer" value="" optional="true" label="precursorWindowSize"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
366 <param argument="-rtWindowInMin" type="float" value="" optional="true" label="rtWindowInMin"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
367 <param argument="-scoringBreadthType" type="select" optional="true" label="scoringBreadthType">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
368 <option value="window">Across entire window</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
369 <option value="recal20">Recalibrated (20% gradient)</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
370 <option value="recal">Recalibrated (peak width only)</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
371 <option value="uncal20">Uncalibrated (20% gradient)</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
372 <option value="uncal">Uncalibrated (peak width only)</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
373 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
374 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
375 </conditional>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
376 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
377 <token name="@WINDOW_OPTIONS@">
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
378 #if $options.window.set_window == 'yes'
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
379 #if str($options.window.foffset)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
380 -foffset $options.window.foffset
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
381 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
382 #if str($options.window.poffset)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
383 -poffset $options.window.poffset
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
384 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
385 #if str($options.window.precursorIsolationMargin)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
386 -precursorIsolationMargin $options.window.precursorIsolationMargin
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
387 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
388 #if str($options.window.precursorWindowSize)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
389 -precursorWindowSize $options.window.precursorWindowSize
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
390 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
391 #if str($options.window.rtWindowInMin)
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
392 -rtWindowInMin $options.window.rtWindowInMin
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
393 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
394 #if $options.window.scoringBreadthType
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
395 -scoringBreadthType $options.window.scoringBreadthType
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
396 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
397 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
398 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
399
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
400 <xml name="modification_options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
401 <conditional name="modifications">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
402 <param name="set_modifications" type="select" label="Set Modifications Options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
403 <option value="no">No - use default options</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
404 <option value="yes">Yes</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
405 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
406 <when value="no"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
407 <when value="yes">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
408 <param argument="-fixed" type="select" optional="true" label="Fixed Modification">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
409 <option value="C=57.0214635">C+57 (Carbamidomethyl) C=57.0214635</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
410 <option value="C=58.005479">C+58 (Carboxymethyl) C=58.005479</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
411 <option value="C=45.987721">C+46 (MMTS) C=45.987721</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
412 <option value="C=125.047679">C+125 (NEM) C=125.047679</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
413 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
414 <yield/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
415 <!--
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
416 <param argument="-localizationModification" type="select" optional="true" label="localizationModification">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
417 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
418 -->
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
419 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
420 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
421 </conditional>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
422 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
423 <token name="@MODIFICATION_OPTIONS@">
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
424 #if $options.modifications.set_modifications == 'yes'
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
425 #if $options.modifications.fixed
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
426 -fixed $options.modifications.fixed
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
427 #end if
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
428 -verifyModificationIons $options.modifications.verifyModificationIons
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
429 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
430 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
431
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
432 <xml name="search_options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
433 <conditional name="search">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
434 <param name="set_search" type="select" label="Set Search Options">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
435 <option value="no">No - use default options</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
436 <option value="yes">Yes</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
437 </param>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
438 <when value="no"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
439 <when value="yes">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
440 <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
441 <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
442 <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
443 <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
444 <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
445 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
446 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
447 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
448 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
449 <!--
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
450 <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
451 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
452 -->
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
453 </when>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
454 </conditional>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
455 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
456 <token name="@SEARCH_OPTIONS@">
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
457 #if $options.search.set_search == 'yes'
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
458 -minCharge $options.search.minCharge
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
459 -maxCharge $options.search.maxCharge
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
460 -minLength $options.search.minLength
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
461 -maxLength $options.search.maxLength
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
462 -minEluteTime $options.search.minEluteTime
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
463 -maxMissedCleavage $options.search.maxMissedCleavage
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
464 -minQuantitativeIonNumber $options.search.minQuantitativeIonNumber
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
465 -minNumOfQuantitativePeaks $options.search.minNumOfQuantitativePeaks
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
466 -numberOfQuantitativePeaks $options.search.numberOfQuantitativePeaks
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
467 ## -addDecoysToBackground $options.search.addDecoysToBackground
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
468 ## -dontRunDecoys $options.search.dontRunDecoys
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
469 #end if
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
470 </token>
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
471
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
472 <xml name="options_section">
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
473 <section name="options" title="Parameter Settings" expanded="false">
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
474 <expand macro="common_options"/>
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
475 <expand macro="mass_library_tolerance"/>
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
476 <expand macro="percolator_options"/>
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
477 <expand macro="peak_options"/>
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
478 <expand macro="window_options"/>
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
479 <expand macro="modification_options"/>
2
174886084dc5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit e3a6bfbf90e9ee3efeb6ff6517074bcc69f8d424"
jjohnson
parents: 1
diff changeset
480 <expand macro="search_options"/>
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
481 </section>
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
482 </xml>
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
jjohnson
parents: 0
diff changeset
483
0
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
484 <xml name="libexport">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
485 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
486 </xml>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
487 <token name="@MSCONVERT_CMD@"><![CDATA[
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
488 msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
489 ]]>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
490 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
491 <token name="@MSCONVERT_RAW@"><![CDATA[
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
492 mzML conversion from RAW requires special options: @MSCONVERT_CMD@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
493 ]]>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
494 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
495 <token name="@MSCONVERT_HELP@"><![CDATA[
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
496
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
497 The MSConvert command can be used to deconvolute DIA raw files. You need to use these options
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
498
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
499 ::
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
500
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
501 @MSCONVERT_CMD@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
502
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
503 ]]>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
504 </token>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
jjohnson
parents:
diff changeset
505 </macros>