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planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty
author lain
date Fri, 03 Mar 2023 14:10:24 +0000
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1 <tool id="ms_to_peakforest_it" name="MS To PeakForest IT" tool_type="interactive" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>
3 adds you MS spectrum to peakforest.
4 </description>
5 <macros>
6 <token name="@VERSION_SUFFIX@">0</token>
7 <import>macros.xml</import>
8 </macros>
9 <requirements>
10 <requirement type="package" version="3.10">python</requirement>
11 <requirement type="package">pyyaml</requirement>
12 </requirements>
13 <entry_points>
14 <entry_point name="MS to PeakForest, with ${','.join(str(i.name) for i in $input)}" requires_domain="True">
15 <port>8000</port>
16 <url>/</url>
17 </entry_point>
18 </entry_points>
19 <version_command>
20 <![CDATA[
21 python3 '$__tool_directory__/server.py' --version | head -n 1
22 ]]>
23 </version_command>
24 <command>
25 @MS2PF_COMMON_CMD@
26 </command>
27 <inputs>
28 <expand macro="ms2pf_inputs" />
29 </inputs>
30 <outputs>
31 <data name="ms2pfout" format="txt"
32 label="${tool.name} on ${','.join(i.name for i in $input)}"
33 />
34 <data name="json_output" format="json"
35 label="JSON ${tool.name} on ${','.join(i.name for i in $input)}.json"
36 >
37 <filter>do_output_json</filter>
38 </data>
39 </outputs>
40 <tests>
41 </tests>
42 <help>
43 <![CDATA[
44 .. class:: infomark
45
46 **Authors** Lain Pavot (lain.pavot@inrae.fr)
47
48 .. class:: infomark
49
50 ---------------------------------------------------
51
52 ==============
53 MS2 validation
54 ==============
55
56 -----------
57 Description
58 -----------
59
60
61 -----------------
62 Workflow position
63 -----------------
64
65 --------------
66 Upstream tools
67 --------------
68
69 +-------------------------+-----------------+--------+------------+
70 | Name | output file | format | parameter |
71 +=========================+=================+========+============+
72 | ms2snoop | tsv | TSV | NA |
73 +-------------------------+-----------------+--------+------------+
74 | abinitfragnot | tsv | TSV | NA |
75 +-------------------------+-----------------+--------+------------+
76
77 ----------------
78 Downstream tools
79 ----------------
80
81 +-------------------------+-----------------+--------+------------+
82 | Name | output file | format | parameter |
83 +=========================+=================+========+============+
84 | NA | NA | NA | NA |
85 +-------------------------+-----------------+--------+------------+
86
87
88 -----------
89 Input files
90 -----------
91
92 +----------------------------------------------+------------+
93 | Parameter : num + label | Format |
94 +===========================+==================+============+
95 | Output from ms2snoop or fragnot | TSV,CSV |
96 +----------------------------------------------+------------+
97
98 ----------
99 Parameters
100 ----------
101
102 input
103 | The file to process. Should contain spectra with mz, intensities and
104 annotations
105
106 method
107 | The method parameter tells which method was used. The value will
108 be the default value in the peakforest form.
109
110 peakforest-url
111 | The peakforest-url parameter tells which instance of peakforest to
112 interact with
113
114 scan_type
115 | The scan_type parameter which kind of scan was used. The value will
116 be the default value in the peakforest form.
117
118 polarity
119 | The polarity parameter which polarity was used. The value will
120 be the default value in the peakforest form.
121
122 name
123 | The name parameter provides names each spectra.
124
125
126 ------------
127 Output files
128 ------------
129
130 There is not output file. When you run this tool, keep waiting until the
131 « click here to display » link appears.
132
133 Click on the link to display peakforest form.
134
135 --------------
136 Changelog/News
137 --------------
138
139 1.0.0
140 | First version, published on the toolshed.
141
142 ]]>
143 </help>
144 </tool>