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comparison metaquantome_sample.xml @ 5:5bc492a15b8b draft

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author galaxyp
date Thu, 07 Feb 2019 17:54:28 -0500
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4:80ce9ca55697 5:5bc492a15b8b
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool id="sample" name="metaQuantome: create samples file" version="@VERSION@.3">
3 <description></description>
4 <macros>
5 <token name="@VERSION@">1.1.2</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@VERSION@">megahit</requirement>
9 </requirements>
10 <version_command>megahit --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 #set $samp_header = 'group\tcolnames'
13 echo -e '${samp_header}' > samp_file.tab;
14 #if $samps_args.samps_src == 'build':
15 #for $s in $samps_args.samps
16 #set $sample = str($s.group_name) + '\t' + str($s.col_names)
17 echo -e '${sample}' >> samp_file.tab;
18 #end for
19 #else:
20 #for $s in $samps_args.samps
21 cat ${samps_args.file} | cut -f ${s.col_names} |
22 head -n 1 | tr '\t' ',' |
23 cat <(echo -e -n "${s.group_name}\t") - >> samp_file.tab;
24 #end for
25 #end if
26 ]]></command>
27 <inputs>
28 <conditional name="samps_args">
29 <param name="samps_src" type="select" label="Sample file creation method">
30 <option value="build">Specify samples</option>
31 <option value="history">Select samples from existing file's header</option>
32 </param>
33 <when value="build">
34 <repeat name="samps" title="Samples">
35 <param name="group_name" type="text" label="Group name" />
36 <param name="col_names" type="text" label="Column" help="Specify the column names of the sample file. Use commas to separate multiple columns." />
37 </repeat>
38 </when>
39 <when value="history">
40 <param name="file" type="data" format="tabular" label="File with group name headers" help="Ex: moFF tool output (headers: peptide X737NS X737WS)" />
41 <repeat name="samps" title="Samples">
42 <param name="group_name" type="text" label="Group name" />
43 <param name="col_names" type="data_column" multiple="true" data_ref="file" label="Column" help="Specify the column indices of the file's header" />
44 </repeat>
45 </when>
46 </conditional>
47 </inputs>
48 <outputs>
49 <data format="tabular" name="samples_file" from_work_dir="samp_file.tab" label="${tool.name} ${on_string}" />
50 </outputs>
51 <tests>
52 <test>
53 <param name="samps_src" value="build" />
54 <repeat name="samps">
55 <param name="group_name" value="NS"/>
56 <param name="col_names" value="X737NS,X852NS,X867NS"/>
57 </repeat>
58 <repeat name="samps">
59 <param name="group_name" value="WS"/>
60 <param name="col_names" value="X737WS,X852WS,X867WS"/>
61 </repeat>
62 <output name="samples_file" file="samples.tab" ftype="tabular"/>
63 </test>
64 <test>
65 <param name="samps_src" value="history" />
66 <param name="file" value="int_737_test.tab" ftype="tabular" />
67 <repeat name="samps">
68 <param name="group_name" value="NS"/>
69 <param name="col_names" value="3,5,7"/>
70 </repeat>
71 <repeat name="samps">
72 <param name="group_name" value="WS"/>
73 <param name="col_names" value="2,4,6"/>
74 </repeat>
75 <output name="samples_file" file="samples.tab" ftype="tabular" />
76 </test>
77 </tests>
78 <help><![CDATA[
79 metaQuantome: create samples file
80 ===================
81
82 The *create samples file* module is used to generate the *samples file* input file for the metaQuantome workflow. This input file is used to specify which column names are affilated with which experimental groups.
83
84 *Create samples file*
85
86 ===== ====================
87 group colnames
88 ===== ====================
89 NS X737NS,X852NS,X867NS
90 WS X737WS,X852WS,X867WS
91 ===== ====================
92
93
94 There are two methods for generating this input file:
95
96 1. **Specify Samples** You may specify the samples by providing the group names (ex: NS *no sucrose* and WS *with sucrose*) and each of their affilated column names (ex: X737WS, X737NS, etc...) from the input files (e.g., peptide intensity *int.tab*).
97
98 2. **Select samples from existing file's header** Alternatively, you can indicate the column indices of the selected headers for each experimental group (ex: columns 1, 3, and 5 for NS; columns 2, 4, and 6 for WS). You need to specify which file from the history you are referencing. An example is shown below.
99
100 *Example int.tab file*
101 ============ ====== ====== ====== ====== ====== ======
102 peptide X737WS X737NS X852WS X852NS X867WS X867NS
103 ============ ====== ====== ====== ====== ====== ======
104 LPGQQHGTPSAK 1 2 3 4 5 6
105 ELPGLAALTDK 7 8 9 10 11 12
106 ============ ====== ====== ====== ====== ====== ======
107
108
109 Questions, Comments, Problems, Kudos
110 ------------------------------------
111
112 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
113 ]]></help>
114 <citations>
115 <citation type="doi">10.1093/bioinformatics/btv033</citation>
116 </citations>
117 </tool>