Mercurial > repos > galaxyp > metaquantome_sample

annotate metaquantome_sample.xml @ 6:06f6826d380c draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
author galaxyp
date Mon, 18 Mar 2024 12:34:10 +0000
parents c1343e3389ca
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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c1343e3389ca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 9204193c3442e427c149b90f15fe3a56fc9802e9"
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1 <tool id="metaquantome_sample" name="metaQuantome: create samples file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
ac3511167a71 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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2 <description> by specifying the experiment's groups and associated column names</description>
ac3511167a71 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
6
06f6826d380c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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6 <expand macro="xrefs"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #set $samp_header = 'group\tcolnames'
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9 echo -e '${samp_header}' > samp_file.tab;
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10 #if $samps_args.samps_src == 'build':
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11 #for $s in $samps_args.samps
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12 #set $sample = str($s.group_name) + '\t' + str($s.col_names)
ac3511167a71 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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13 echo -e '${sample}' >> samp_file.tab;
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14 #end for
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15 #else:
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16 #for $s in $samps_args.samps
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17 cat ${samps_args.file} | cut -f ${s.col_names} |
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18 head -n 1 | tr '\t' ',' |
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19 cat <(echo -e -n "${s.group_name}\t") - >> samp_file.tab;
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20 #end for
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21 #end if
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22 ]]></command>
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23 <inputs>
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24 <conditional name="samps_args">
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25 <param name="samps_src" type="select" label="Sample file creation method">
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26 <option value="build">Manually specify experimental conditions and samples</option>
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27 <option value="history">Select samples from the header of an existing file</option>
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28 </param>
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29 <when value="build">
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30 <repeat name="samps" title="Samples">
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31 <param name="group_name" type="text" label="Group name" help="Provide a name for the experimental condition."/>
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32 <param name="col_names" type="text" label="Column"
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33 help="Give a comma-separated list of the column names that correspond to samples within the experimental condition." />
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34 </repeat>
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35 </when>
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36 <when value="history">
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37 <param name="file" type="data" format="tabular" label="File with group name headers" help="Ex: moFF tool output (headers: peptide X737NS X737WS)" />
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38 <repeat name="samps" title="Samples">
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39 <param name="group_name" type="text" label="Group name" />
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40 <param name="col_names" type="data_column" multiple="true" data_ref="file" label="Column" help="Specify the column indices of the file's header" />
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41 </repeat>
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42 </when>
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43 </conditional>
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44 </inputs>
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45 <outputs>
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46 <data format="tabular" name="samples_file" from_work_dir="samp_file.tab" label="${tool.name} ${on_string}" />
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="samps_src" value="build" />
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51 <repeat name="samps">
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52 <param name="group_name" value="NS"/>
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53 <param name="col_names" value="X737NS,X852NS,X867NS"/>
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54 </repeat>
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55 <repeat name="samps">
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56 <param name="group_name" value="WS"/>
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57 <param name="col_names" value="X737WS,X852WS,X867WS"/>
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58 </repeat>
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59 <output name="samples_file" file="samples.tab" ftype="tabular"/>
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60 </test>
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61 <test>
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62 <param name="samps_src" value="history" />
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63 <param name="file" value="int_737_test.tab" ftype="tabular" />
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64 <repeat name="samps">
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65 <param name="group_name" value="NS"/>
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66 <param name="col_names" value="3,5,7"/>
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67 </repeat>
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68 <repeat name="samps">
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69 <param name="group_name" value="WS"/>
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70 <param name="col_names" value="2,4,6"/>
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71 </repeat>
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72 <output name="samples_file" file="samples.tab" ftype="tabular" />
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73 </test>
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74 </tests>
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75 <help><![CDATA[
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76 metaQuantome: create samples file
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77 =================================
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78
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79 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.
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80
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81 *Create samples file*
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82 ===== ====================
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83 group colnames
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84 ===== ====================
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85 NS X737NS,X852NS,X867NS
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86 WS X737WS,X852WS,X867WS
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87 ===== ====================
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88
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89
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90 There are two methods for generating this input file:
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91
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92 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*).
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93
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94
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95 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.
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96
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97 *int.tab file*
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98 ============ ====== ====== ====== ====== ====== ======
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99 peptide X737WS X737NS X852WS X852NS X867WS X867NS
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100 ============ ====== ====== ====== ====== ====== ======
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101 LPGQQHGTPSAK 1 2 3 4 5 6
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102 ELPGLAALTDK 7 8 9 10 11 12
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103 ============ ====== ====== ====== ====== ====== ======
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104
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105
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106 Questions, Comments, Problems, Kudos
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107 ------------------------------------
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108
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109 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
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110 ]]></help>
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111 <citations>
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112 <citation type="doi">10.1093/bioinformatics/btv033</citation>
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113 </citations>
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114 </tool>