Mercurial > repos > galaxyp > metaquantome_sample

comparison metaquantome_sample.xml @ 0:ac3511167a71 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/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
author galaxyp
date Thu, 25 Apr 2019 13:50:09 -0400
parents
children c1343e3389ca
comparison
equal deleted inserted replaced
-1:000000000000 0:ac3511167a71
1 <tool id="metaquantome_sample" name="metaQuantome: create samples file" version="@GVERSION@">
2 <description> by specifying the experiment's groups and associated column names</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <command detect_errors="exit_code"><![CDATA[
7 #set $samp_header = 'group\tcolnames'
8 echo -e '${samp_header}' > samp_file.tab;
9 #if $samps_args.samps_src == 'build':
10 #for $s in $samps_args.samps
11 #set $sample = str($s.group_name) + '\t' + str($s.col_names)
12 echo -e '${sample}' >> samp_file.tab;
13 #end for
14 #else:
15 #for $s in $samps_args.samps
16 cat ${samps_args.file} | cut -f ${s.col_names} |
17 head -n 1 | tr '\t' ',' |
18 cat <(echo -e -n "${s.group_name}\t") - >> samp_file.tab;
19 #end for
20 #end if
21 ]]></command>
22 <inputs>
23 <conditional name="samps_args">
24 <param name="samps_src" type="select" label="Sample file creation method">
25 <option value="build">Manually specify experimental conditions and samples</option>
26 <option value="history">Select samples from the header of an existing file</option>
27 </param>
28 <when value="build">
29 <repeat name="samps" title="Samples">
30 <param name="group_name" type="text" label="Group name" help="Provide a name for the experimental condition."/>
31 <param name="col_names" type="text" label="Column"
32 help="Give a comma-separated list of the column names that correspond to samples within the experimental condition." />
33 </repeat>
34 </when>
35 <when value="history">
36 <param name="file" type="data" format="tabular" label="File with group name headers" help="Ex: moFF tool output (headers: peptide X737NS X737WS)" />
37 <repeat name="samps" title="Samples">
38 <param name="group_name" type="text" label="Group name" />
39 <param name="col_names" type="data_column" multiple="true" data_ref="file" label="Column" help="Specify the column indices of the file's header" />
40 </repeat>
41 </when>
42 </conditional>
43 </inputs>
44 <outputs>
45 <data format="tabular" name="samples_file" from_work_dir="samp_file.tab" label="${tool.name} ${on_string}" />
46 </outputs>
47 <tests>
48 <test>
49 <param name="samps_src" value="build" />
50 <repeat name="samps">
51 <param name="group_name" value="NS"/>
52 <param name="col_names" value="X737NS,X852NS,X867NS"/>
53 </repeat>
54 <repeat name="samps">
55 <param name="group_name" value="WS"/>
56 <param name="col_names" value="X737WS,X852WS,X867WS"/>
57 </repeat>
58 <output name="samples_file" file="samples.tab" ftype="tabular"/>
59 </test>
60 <test>
61 <param name="samps_src" value="history" />
62 <param name="file" value="int_737_test.tab" ftype="tabular" />
63 <repeat name="samps">
64 <param name="group_name" value="NS"/>
65 <param name="col_names" value="3,5,7"/>
66 </repeat>
67 <repeat name="samps">
68 <param name="group_name" value="WS"/>
69 <param name="col_names" value="2,4,6"/>
70 </repeat>
71 <output name="samples_file" file="samples.tab" ftype="tabular" />
72 </test>
73 </tests>
74 <help><![CDATA[
75 metaQuantome: create samples file
76 =================================
77
78 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 the column names used for each experimental group. These column names are referenced when handling the input data and performing statistical analysis. An example file is shown below.
79
80 *Create samples file*
81 ===== ====================
82 group colnames
83 ===== ====================
84 NS X737NS,X852NS,X867NS
85 WS X737WS,X852WS,X867WS
86 ===== ====================
87
88
89 There are two methods for generating this input file:
90
91 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*).
92
93
94 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 3, 5, and 7 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.
95
96 *int.tab file*
97 ============ ====== ====== ====== ====== ====== ======
98 peptide X737WS X737NS X852WS X852NS X867WS X867NS
99 ============ ====== ====== ====== ====== ====== ======
100 LPGQQHGTPSAK 1 2 3 4 5 6
101 ELPGLAALTDK 7 8 9 10 11 12
102 ============ ====== ====== ====== ====== ====== ======
103
104
105 Questions, Comments, Problems, Kudos
106 ------------------------------------
107
108 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
109 ]]></help>
110 <citations>
111 <citation type="doi">10.1093/bioinformatics/btv033</citation>
112 </citations>
113 </tool>