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