Mercurial > repos > galaxyp > metaquantome_sample

annotate metaquantome_sample.xml @ 0:ac3511167a71 draft

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