Mercurial > repos > galaxyp > openms_eicextractor
annotate EICExtractor.xml @ 16:c0f39306c687 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
---|---|
date | Fri, 14 Jun 2024 21:40:11 +0000 |
parents | f253d41d9170 |
children |
rev | line source |
---|---|
7
72e0bc55a462
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents:
3
diff
changeset
|
1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
2 <!--Proposed Tool Section: [Quantitation]--> |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3 <tool id="EICExtractor" name="EICExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
4 <description>Extracts intensities from dedicates positions in a LC/MS map</description> |
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
5 <macros> |
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
6 <token name="@EXECUTABLE@">EICExtractor</token> |
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
7 <import>macros.xml</import> |
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
8 </macros> |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
9 <expand macro="requirements"/> |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
10 <expand macro="stdio"/> |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
12 @EXT_FOO@ |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
13 #import re |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
14 |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
15 ## Preprocessing |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
16 mkdir in_cond.in && |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
17 #if $in_cond.in_select == "no" |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
20 #else |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
22 #end if |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
23 #if $in_header_cond.in_header: |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
24 mkdir in_header_cond.in_header && |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
25 #if $in_header_cond.in_header_select == "no" |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
26 mkdir ${' '.join(["'in_header_cond.in_header/%s'" % (i) for i, f in enumerate($in_header_cond.in_header) if f])} && |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
27 ${' '.join(["cp '%s' 'in_header_cond.in_header/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])} |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
28 #else |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
29 cp '$in_header_cond.in_header' 'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)' && |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
30 #end if |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
31 #end if |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
32 mkdir pos && |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
33 cp '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' && |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
34 mkdir out && |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
35 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
36 mkdir auto_rt_out_debug_TIC && |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
37 #end if |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
38 |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
39 ## Main program call |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
40 |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
41 set -o pipefail && |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
42 @EXECUTABLE@ -write_ctd ./ && |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
43 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
44 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
45 -in |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
46 #if $in_cond.in_select == "no" |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
47 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
48 #else |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
49 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
50 #end if |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
51 #if $in_header_cond.in_header: |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
52 -in_header |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
53 #if $in_header_cond.in_header_select == "no" |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
54 ${' '.join(["'in_header_cond.in_header/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])} |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
55 #else |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
56 'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)' |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
57 #end if |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
58 #end if |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
59 -pos |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
60 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
61 -out |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
62 'out/output.${gxy2omsext("csv")}' |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
63 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
64 -auto_rt:out_debug_TIC |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
65 'auto_rt_out_debug_TIC/output.${gxy2omsext("mzml")}' |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
66 #end if |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
67 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
68 | tee '$stdout' |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
69 #end if |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
70 |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
71 ## Postprocessing |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
72 && mv 'out/output.${gxy2omsext("csv")}' '$out' |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
73 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
74 && mv 'auto_rt_out_debug_TIC/output.${gxy2omsext("mzml")}' '$auto_rt_out_debug_TIC' |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
75 #end if |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
76 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
77 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
78 #end if]]></command> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
79 <configfiles> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
80 <inputs name="args_json" data_style="paths"/> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
81 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
82 </configfiles> |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
83 <inputs> |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
84 <conditional name="in_cond"> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
85 <param name="in_select" type="select" label="Run tool in batch mode for -in"> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
86 <option value="no">No: process all datasets jointly</option> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
87 <option value="yes">Yes: process each dataset in an independent job</option> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
88 </param> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
89 <when value="no"> |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
90 <param argument="-in" type="data" format="mzml" multiple="true" label="Input raw data file" help=" select mzml data sets(s)"/> |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
91 </when> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
92 <when value="yes"> |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
93 <param argument="-in" type="data" format="mzml" label="Input raw data file" help=" select mzml data sets(s)"/> |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
94 </when> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
95 </conditional> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
96 <conditional name="in_header_cond"> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
97 <param name="in_header_select" type="select" label="Run tool in batch mode for -in_header"> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
98 <option value="no">No: process all datasets jointly</option> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
99 <option value="yes">Yes: process each dataset in an independent job</option> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
100 </param> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
101 <when value="no"> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
102 <param argument="-in_header" type="data" format="txt" multiple="true" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
103 </when> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
104 <when value="yes"> |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
105 <param argument="-in_header" type="data" format="txt" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/> |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
106 </when> |
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
107 </conditional> |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
108 <param argument="-pos" type="data" format="edta" label="Input config file stating where to find signal" help=" select edta data sets(s)"/> |
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
109 <param argument="-rt_tol" type="float" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/> |
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
110 <param argument="-mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/> |
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
111 <param argument="-rt_collect" type="integer" value="1" label="# of scans up & down in RT from highest point for ppm estimation in result" help=""/> |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
112 <section name="auto_rt" title="Parameters for automatic detection of injection RT peaks (no need to specify them in 'pos' input file)" help="" expanded="false"> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
113 <param name="enabled" argument="-auto_rt:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help=""/> |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
114 <param name="FHWM" argument="-auto_rt:FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="Gaussian smoothing filter with this width is applied to TIC"/> |
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
115 <param name="SNThreshold" argument="-auto_rt:SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="Higher thesholds will result in less peaks"/> |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
116 </section> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
117 <expand macro="adv_opts_macro"> |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
118 <param argument="-out_separator" type="text" value="," label="Separator character for output CSV file" help=""> |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
119 <expand macro="list_string_san" name="out_separator"/> |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
120 </param> |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
121 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
122 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> |
15
f253d41d9170
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
123 <expand macro="list_string_san" name="test"/> |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
124 </param> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
125 </expand> |
13
0546885ddaf9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents:
11
diff
changeset
|
126 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
127 <option value="out_debug_TIC_FLAG">out_debug_TIC (Optional output file (for first input) containing the smoothed TIC, S/N levels and picked RT positions)</option> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
128 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
129 </param> |
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
130 </inputs> |
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
131 <outputs> |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
132 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
133 <data name="auto_rt_out_debug_TIC" label="${tool.name} on ${on_string}: auto_rt:out_debug_TIC" format="mzml"> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
134 <filter>OPTIONAL_OUTPUTS is not None and "out_debug_TIC_FLAG" in OPTIONAL_OUTPUTS</filter> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
135 </data> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
136 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
137 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
138 </data> |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
139 </outputs> |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
140 <tests> |
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
141 <test expect_num_outputs="1"> |
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
142 <!-- just using some random test data --> |
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
143 <param name="adv_opts|test" value="true"/> |
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
144 <param name="in" value="spectra.mzML"/> |
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
145 <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/> |
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
146 <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/> |
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
147 </test> |
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
148 </tests> |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
149 <help><![CDATA[Extracts intensities from dedicates positions in a LC/MS map |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
150 |
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
151 |
16
c0f39306c687
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
152 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_EICExtractor.html]]></help> |
11
2bd3c83eed94
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
153 <expand macro="references"/> |
0
0cdc3e405e3c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
154 </tool> |