annotate metaquantome_viz.xml @ 3:944b43462104 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
author galaxyp
date Tue, 24 Nov 2020 15:08:30 +0000
parents 02da24eac445
children 1199751329b0
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6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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1 <tool id="metaquantome_viz" name="metaQuantome: visualize" version="@GVERSION@">
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2 <description>taxonomic analysis, functional analysis, and function-taxonomy analysis results</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="barcol">
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6 <param argument="--barcol" type="select" label="Color for the bar fill">
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7 <option value="1">Blue</option>
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8 <option value="2">Orange</option>
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9 <option value="3">Yellow</option>
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10 <option value="4">Red</option>
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11 <option value="5">Violet</option>
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12 <option value="6">Black</option>
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13 <help>
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14 These same colors are also used in the heatmap and PCA plot,
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15 so the colors can be tweaked to match. Note that these colors
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16 are coded as 1 through 6 in the command line tool.
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17 </help>
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18 </param>
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19 </xml>
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20 <xml name="common_bar_params">
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21 <param argument="--meancol" type="text" label="Mean intensity column name"
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22 help="Mean intensity column name for desired experimental condition">
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23 <validator type="empty_field"/>
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24 </param>
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25 <param argument="--nterms" type="integer"
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26 value="5" min="1" optional="true"
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27 label="Number of terms to display"
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28 help="leave blank for all terms"/>
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29 </xml>
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30 <xml name="common_volc_params">
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31 <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe">
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32 <validator type="empty_field"/>
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33 </param>
1
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34 <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
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35 <validator type="empty_field"/>
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36 </param>
0
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37 <param argument="--textannot" type="text" optional="true" label="Name of the annotation column"
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38 help="Provides text annotatation for the plot. Optional. If missing, no text will be plotted."/>
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39 <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false"
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40 label="Flip the fold change (i.e., multiply log fold change by -1)"/>
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41 </xml>
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42 <xml name="common_heatmap_params">
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43 <conditional name="heatmap">
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44 <param argument="--filter_to_sig" type="boolean" checked="false"
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45 label="Only plot significant term" help="Necessitates use of results from `test`"/>
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46 <when value="true">
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47 <param argument="--alpha" type="float"
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48 value="0.05" min="0.0" max="1.0"
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49 label="The q-value significance level"/>
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50 <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
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51 <validator type="empty_field"/>
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52 </param>
0
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53 </when>
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54 <when value="false">
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55 <!-- do nothing -->
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56 </when>
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57 </conditional>
2
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58 <param argument="--feature_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree."/>
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59 <param argument="--sample_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree."/>
0
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60 </xml>
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61 <xml name="pca_calcsep">
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62 <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false"
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63 label="Calculate separation between groups and include in title?"/>
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64 </xml>
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65 <xml name="target_onto">
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66 <param argument="--target_onto" type="select" optional="false"
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67 label="GO category to restrict to">
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68 <help>
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69 Only the values from this category
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70 of GO terms will be displayed.
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71 </help>
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72 <option value="bp">Biological Process</option>
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73 <option value="mf">Molecular Function</option>
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74 <option value="cc">Cellular Component</option>
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75 </param>
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76 </xml>
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77 </macros>
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78 <expand macro="requirements" />
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79 <command detect_errors="exit_code"><![CDATA[
3
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80 #import re
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81 #set $safename = re.sub('[^\w\-_\.]', '_', $infile.element_identifier)
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82 ln -s '$infile' '$safename'
1
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83 &&
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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84 metaquantome viz
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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85 --samps '$samps'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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86 --mode '$mode_args.mode'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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87 #if str($mode_args.mode) == 'f'
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88 --ontology='$mode_args.ontology'
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89 #end if
3
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90 --infile='$safename'
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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91 --plottype='$mode_args.plot.plottype'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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92 #if $mode_args.plot.plottype == 'bar':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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93 #if str($mode_args.mode) == 't':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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94 --target_rank='$mode_args.plot.target_rank'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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95 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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96 --meancol='$mode_args.plot.meancol'
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97 #if str($mode_args.plot.nterms) == '':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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98 --nterms='all'
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99 #else
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100 --nterms=$mode_args.plot.nterms
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101 #end if
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102 #if str($mode_args.mode) == 'f':
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103 --target_onto='$mode_args.plot.target_onto'
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104 #end if
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105 --barcol=$mode_args.plot.barcol
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106 #elif $mode_args.plot.plottype == 'volcano':
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107 --fc_name='$mode_args.plot.fc_name'
1
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108 --fc_corr_p='$mode_args.plot.fc_corr_p'
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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109 #if $mode_args.plot.textannot:
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110 --textannot='$mode_args.plot.textannot'
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111 #end if
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112 $mode_args.plot.flip_fc
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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113 #if $mode_args.mode == 'f':
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114 $mode_args.plot.gosplit
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115 #end if
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116 #elif $mode_args.plot.plottype == 'heatmap':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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117 #if $mode_args.plot.heatmap.filter_to_sig:
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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118 --filter_to_sig
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119 --alpha=$mode_args.plot.heatmap.alpha
1
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120 --fc_corr_p='mode_args.plot.fc_corr_p'
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
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121 #end if
3
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122 #if $mode_args.plot.feature_cluster_size:
1
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
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123 --feature_cluster_size='$mode_args.plot.feature_cluster_size'
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
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124 #end if
3
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125 #if $mode_args.plot.sample_cluster_size:
1
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126 --sample_cluster_size='$mode_args.plot.sample_cluster_size'
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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127 #end if
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128 #elif $mode_args.plot.plottype == 'pca':
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129 $mode_args.plot.calculate_sep
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130 #elif $mode_args.plot.plottype == 'ft_dist':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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131 --barcol='$mode_args.plot.barcol'
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132 --whichway='$mode_args.plot.margin.whichway'
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133 --meancol='$mode_args.plot.meancol'
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134 #if $mode_args.plot.margin.term.id_or_name == 'id':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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135 --id='$mode_args.plot.margin.term.id'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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136 #else:
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137 --name='$mode_args.plot.margin.term.name'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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138 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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139 #if $mode_args.plot.margin.whichway == 't_dist':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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140 --target_rank='$mode_args.plot.margin.target_rank'
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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141 #end if
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142 #if $mode_args.plot.margin.whichway == 'f_dist':
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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143 --target_onto=$mode_args.plot.margin.target_onto
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144 #end if
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145 #end if
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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146 #if $width:
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147 --width=$width
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148 #end if
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149 #if $height:
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150 --height=$height
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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151 #end if
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152 --img='outfile.png'
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153 --tabfile='plotdata.tab' &&
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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154 mkdir '${ wrapped_outfile.files_path }' &&
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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155 cp outfile.png '${ wrapped_outfile.files_path }' &&
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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156 echo "<!DOCTYPE html>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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157 <html>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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158 <body>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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159 <img src=\"outfile.png\" width=600>
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160 <br>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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161 <p>To download the image, right-click and choose \"Save image as...\"</p>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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162 <br>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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163 <p>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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164 If text is cut off or the plot is not displaying properly,
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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165 the easiest fix is to increase the plot dimensions
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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166 </p>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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167 </body>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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168 </html>" > wrapped_outfile.html
3
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169 && >&2 ls
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170 #if $mode_args.plot.plottype in ["heatmap"]
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171 && mv 'feature_cluster_${safename}.txt' '$heatmap_feature_cluster'
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
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172 && mv 'sample_cluster_${safename}.txt' '$heatmap_sample_cluster'
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
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173 #end if
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174 #if $mode_args.plot.plottype in ["pca"]
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175 && mv 'PC_data_${safename}.txt' '$pca_sample_cluster'
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
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176 #end if
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177
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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178 ]]></command>
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179 <inputs>
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180 <param argument="--infile" type="data"
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181 format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/>
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182 <expand macro="SAMPS"/>
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183 <conditional name="mode_args">
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184 <param argument="--mode" type="select" label="Mode">
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185 <option value="f">Functional analysis</option>
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186 <option value="t">Taxonomic analysis</option>
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187 <option value="ft">Functional-taxonomic interaction analysis</option>
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188 </param>
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189 <when value="f">
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190 <param name="ontology" type="select" label="Ontology">
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191 <option value="go">Gene Ontology (GO terms)</option>
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192 <option value="ec">Enzyme Commission (EC) numbers</option>
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193 <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
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194 </param>
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195 <conditional name="plot">
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196 <param argument="--plottype" type="select" label="Plot type">
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197 <option value="bar">Bar Chart (bar)</option>
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198 <option value="volcano">Volcano Plot (volcano)</option>
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199 <option value="heatmap">Heatmap (heatmap)</option>
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200 <option value="pca">Principal Components Analysis (pca)</option>
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201 </param>
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202 <when value="bar">
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203 <expand macro="common_bar_params"/>
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204 <expand macro="target_onto"/>
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205 <expand macro="barcol"/>
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206 </when>
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207 <when value="volcano">
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208 <expand macro="common_volc_params"/>
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209 <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false"
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210 label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction GO term categories."/>
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211 </when>
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212 <when value="heatmap">
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213 <expand macro="common_heatmap_params"/>
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214 </when>
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215 <when value="pca">
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216 <expand macro="pca_calcsep"/>
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217 </when>
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218 </conditional>
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219 </when>
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220 <when value="t">
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221 <conditional name="plot">
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222 <param argument="--plottype" type="select" label="Plot type">
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223 <option value="bar">Bar Chart (bar)</option>
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224 <option value="volcano">Volcano Plot (volcano)</option>
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225 <option value="heatmap">Heatmap (heatmap)</option>
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226 <option value="pca">Principal Components Analysis (pca)</option>
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227 </param>
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228 <when value="bar">
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229 <param argument="--target_rank" type="select"
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230 label="Taxonomic rank to restrict to in the plot"
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231 help="possibilities are taken from the input dataset.">
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232 <options from_dataset="infile">
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233 <column name="value" index="2"/>
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234 <filter type="unique_value" name="unique_taxon" column="2"/>
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235 <!-- <filter type="remove_value" value="rank" column="2"/> -->
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236 </options>
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237 </param>
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238 <expand macro="common_bar_params"/>
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239 <expand macro="barcol"/>
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240 </when>
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241 <when value="volcano">
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242 <expand macro="common_volc_params"/>
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243 </when>
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244 <when value="heatmap">
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245 <expand macro="common_heatmap_params"/>
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246 </when>
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247 <when value="pca">
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248 <expand macro="pca_calcsep"/>
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249 </when>
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250 </conditional>
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251 </when>
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252 <when value="ft">
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253 <conditional name="plot">
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254 <param argument="--plottype" type="select" label="Plot type">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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255 <option value="ft_dist" selected="true">Functional Taxonomic Distribution (ft_dist)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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256 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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257 <when value="ft_dist">
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258 <param argument="--meancol" type="text" label="Mean intensity column name"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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259 help="Mean intensity column name for desired experimental condition">
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260 <validator type="empty_field"/>
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261 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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262 <conditional name="margin">
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galaxyp
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263 <param argument="--whichway" type="select" label="which distribution">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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264 <option value="f_dist">functional distribution for a taxon (f_dist)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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265 <option value="t_dist">taxonomic distribution for a function (t_dist)</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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266 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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267 <when value="f_dist">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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268 <conditional name="term">
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269 <param name="id_or_name" type="select" label="">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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270 <option value="id" selected="true">Taxon ID</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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271 <option value="name">Taxon name</option>
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272 </param>
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273 <when value="id">
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274 <param argument="--id" type="select" label="Taxon id">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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275 <options from_dataset="infile">
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276 <column name="value" index="3"/>
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277 <filter type="unique_value" column="3"/>
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278 <!-- <filter type="remove_value" value="tax_id"/> -->
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279 </options>
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280 </param>
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281 </when>
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282 <when value="name">
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283 <param argument="--name" type="select" label="Taxon name">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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284 <options from_dataset="infile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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285 <column name="value" index="4"/>
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286 <filter type="unique_value" column="4"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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287 <!-- <filter type="remove_value" value="taxon_name"/> -->
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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288 </options>
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289 </param>
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290 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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291 </conditional>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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diff changeset
292 <expand macro="target_onto"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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293 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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294 <when value="t_dist">
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diff changeset
295 <conditional name="term">
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296 <param name="id_or_name" type="select" label="">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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297 <option value="id" selected="true">Functional term ID</option>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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298 <option value="name">Functional term name</option>
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299 </param>
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diff changeset
300 <when value="id">
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301 <param argument="--id" type="select" label="Functional term id">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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302 <options from_dataset="infile">
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303 <column name="value" index="0"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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304 <filter type="unique_value" column="0"/>
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galaxyp
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305 <!-- <filter type="remove_value" value="go_id"/> -->
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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306 </options>
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307 </param>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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308 </when>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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309 <when value="name">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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310 <param argument="--name" type="select" label="Functional term name">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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311 <options from_dataset="infile">
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312 <column name="value" index="1"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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313 <filter type="unique_value" column="1"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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314 <!-- <filter type="remove_value" value="name"/> -->
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315 </options>
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316 </param>
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317 </when>
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318 </conditional>
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319 <param argument="--target_rank" type="select"
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320 label="Taxonomic rank to restrict to in the plot"
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321 help="possibilities are taken from the input dataset.">
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322 <options from_dataset="infile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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323 <column name="value" index="5"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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324 <filter type="unique_value" name="unique_taxon" column="5"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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325 <!-- <filter type="remove_value" value="rank" column="5"/> -->
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326 </options>
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327 </param>
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328 </when>
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329 </conditional>
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330 <expand macro="barcol"/>
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331 </when>
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332 </conditional>
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333 </when>
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334 </conditional>
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335 <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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336 <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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337 </inputs>
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338 <outputs>
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339 <data format="html" name="wrapped_outfile"
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diff changeset
340 label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html"
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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diff changeset
341 from_work_dir="wrapped_outfile.html"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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diff changeset
342 <data format="tabular" name="plotdata"
3
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
galaxyp
parents: 2
diff changeset
343 label="${tool.name} on ${on_string} ${mode_args.plot.plottype}: plot data"
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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diff changeset
344 from_work_dir="plotdata.tab">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
345 <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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diff changeset
346 </data>
1
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
347
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
348 <data format="tabular" name="heatmap_feature_cluster"
3
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
galaxyp
parents: 2
diff changeset
349 label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} feature cluster data">
1
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
350 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
351 </data>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
352 <data format="tabular" name="heatmap_sample_cluster"
3
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
galaxyp
parents: 2
diff changeset
353 label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} sample cluster data">
1
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
354 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
355 </data>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
356
3
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
galaxyp
parents: 2
diff changeset
357 <data format="tabular" name="pca_sample_cluster"
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
galaxyp
parents: 2
diff changeset
358 label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} sample cluster data">
1
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
359 <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
360 </data>
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
361
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
362 </outputs>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
363 <tests>
3
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
galaxyp
parents: 2
diff changeset
364 <test expect_num_outputs="2">
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
365 <param name="infile" value="tax_filt_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
366 <param name="mode" value="t" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
367 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
368 <param name="plottype" value="bar" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
369 <param name="target_rank" value="genus" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
370 <param name="meancol" value="NS_mean" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
371 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
372 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
373 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
374 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
375 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
376 </test>
3
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
galaxyp
parents: 2
diff changeset
377 <test expect_num_outputs="2">
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
378 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
379 <param name="mode" value="t" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
380 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
381 <param name="plottype" value="volcano" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
382 <param name="target_rank" value="genus" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
383 <param name="fc_name" value="log2fc_NS_over_WS" />
1
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
parents: 0
diff changeset
384 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
385 <param name="textannot" value="taxon_name" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
386 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
387 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
388 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
389 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
390 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
391 </test>
3
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
galaxyp
parents: 2
diff changeset
392 <test expect_num_outputs="3">
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
393 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
394 <param name="mode" value="t" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
395 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
396 <param name="plottype" value="heatmap" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
397 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
398 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
399 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
400 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
401 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
402 </test>
3
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
galaxyp
parents: 2
diff changeset
403 <test expect_num_outputs="2">
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
404 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
405 <param name="mode" value="t" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
406 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
407 <param name="plottype" value="pca" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
408 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
409 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
410 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
411 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
412 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
413 </test>
3
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
galaxyp
parents: 2
diff changeset
414 <test expect_num_outputs="2">
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
415 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
416 <param name="mode" value="f" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
417 <param name="ontology" value="go" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
418 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
419 <param name="plottype" value="bar" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
420 <param name="meancol" value="NS_mean" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
421 <param name="target_onto" value="bp"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
422 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
parents:
diff changeset
423 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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424 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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425 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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426 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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427 </test>
3
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
galaxyp
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428 <test expect_num_outputs="2">
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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429 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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430 <param name="mode" value="f" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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431 <param name="ontology" value="go"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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432 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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433 <param name="plottype" value="volcano" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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434 <param name="fc_name" value="log2fc_NS_over_WS" />
1
8c30496a665a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
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435 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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436 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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437 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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438 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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439 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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440 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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441 </test>
3
944b43462104 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
galaxyp
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442 <test expect_num_outputs="1">
0
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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443 <param name="infile" value="tf_filt_out.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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444 <param name="mode" value="ft" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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445 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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446 <param name="plottype" value="ft_dist" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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447 <param name="meancol" value="NS_mean" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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448 <param name="whichway" value="f_dist" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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449 <param name="id_or_name" value="id" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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450 <param name="id" value="1301" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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451 <param name="target_onto" value="bp" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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452 <output name="wrapped_outfile">
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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453 <assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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454 <has_text text="To download the image" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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455 </assert_contents>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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456 </output>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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457 </test>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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458 </tests>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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459 <help><![CDATA[
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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460 metaQuantome viz
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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461 ===================
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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462
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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463 The *viz* module is the final step in the metaQuantome analysis workflow.
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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464 The available visualizations are:
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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465
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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466 - bar plot
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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467 - volcano plot
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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468 - heatmap
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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469 - PCA plot
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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470
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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471 Please consult the manuscript for full details on each of these plots.
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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472
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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473 Questions, Comments, Problems, Kudos
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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474 --------------------------------------
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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475
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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476 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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477 ]]></help>
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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478 <expand macro="citations" />
6cfd42b015b4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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479 </tool>