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1 <tool id='isoplot' name='Isoplot: Generate plots from isocor output' version='0.1.0'>
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2 <requirements>
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3 <requirement type='package' version='1.3.0'>isoplot</requirement>
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4 </requirements>
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5 <command><![CDATA[
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6 isoplot '$datafile' 'galaxy' '$format' --value '$value' --template '$template_file'
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7 #if $SP.generate_barplot:
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8 -bp
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9 #end if
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10 #if $SP.generate_meanplot:
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11 -mb
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12 #end if
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13 #if $SP.generate_heatmap:
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14 -hm
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15 #end if
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16 #if $SP.generate_clustermap:
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17 -cm
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18 #end if
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19 #if $IP.generate_barplot:
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20 -IB
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21 #end i
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22 #if $IP.generate_meanplot:
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23 -IM
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24 #end if
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25 #if $IP.generate_heatmap:
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26 -HM
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27 #end if
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28 #if $stack:
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29 -s
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30 #end if
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31 #if $verbosity:
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32 -v
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33 #end if
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34 #if $annotation:
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35 -a
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36 #end if
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37 -g -z '$output2' > $output1 2> '$output3'
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38 ]]></command>
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39 <inputs>
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40 <param name='datafile' type='data' format='csv, tsv' multiple='true' label='Upload data file' />
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41 <param name='template_file' type='data' format='csv, xlsx' multiple='true' label='Template file' argument='--template'/>
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42 <!--param name='run_name' type='text' label='Run name' /-->
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43 <param name='format' type='select' label='Plot format'>
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44 <option value='pdf'>pdf</option>
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45 <option value='jpeg'>jpeg</option>
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46 <option value='png'>png</option>
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47 <option value='svg'>svg</option>
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48 <option value='html'>html</option>
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49 </param>
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50 <param name='value' type='select' label='Data to plot' >
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51 <option value='corrected_area'>Corrected Area</option>
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52 <option value='isotopologue_fraction'>Isotopologue Fraction</option>
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53 <option value='mean_enrichment'>Mean Enrichment</option>
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54 </param>
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55 <section name='SP' title='Select static plots to generate'>
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56 <param type='boolean' name='generate_barplot' label='Flag to generate barplots' argument='-bp'
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57 optional='true'/>
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58 <param type='boolean' name='generate_meanplot' label='Flag to generate meaned barplots' argument='-mb'
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59 optional='true'/>
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60 <!--<param type='boolean' name='generate_areaplot' label='Flag to generate stacked area plots'
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61 argument='-sa' optional='true'/>/-->
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62 <param type='boolean' name='generate_heatmap' label='Flag to generate heatmap' argument='-hm'
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63 optional='true'/>
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64 <param type='boolean' name='generate_clustermap' label='Flag to generate clustermap' argument='-cm'
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65 optional='true'/>
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66 </section>
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67 <section name='IP' title='Select interactive plots to generate'>
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68 <param type='boolean' name='generate_barplot' label='Flag to generate barplots' argument='-IB'
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69 optional='true'/>
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70 <param type='boolean' name='generate_meanplot' label='Flag to generate meaned barplots' argument='-IM'
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71 optional='true'/>
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72 <!-- <param type='boolean' name='generate_areaplot' label='Flag to generate stacked area plots' argument='-IS'
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73 optional='true'/>-->
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74 <param type='boolean' name='generate_heatmap' label='Flag to generate heatmap' argument='-HM'
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75 optional='true'/>
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76 </section>
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77 <param type='boolean' name='stack' label='Flag to unstack bars in barplots' argument='-s' optional='true'/>
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78 <param type='boolean' name='verbosity' label='Flag to get debug information' argument='-v' optional='true'/>
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79 <param type='boolean' name='annotation' label='Flag to add annotations on the maps' argument='-a'
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80 optional='true'/>
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81 </inputs>
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82 <outputs>
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83 <data name='output1' format='csv' label='Formatted data used for plotting' />
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84 <data name='output2' format='zip' label='Resulting plots' />
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85 <data name='output3' format='txt' label='Run Info' />
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86 </outputs>
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87 <help><![CDATA[
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88
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89 Isoplot2: Plotting isotopic labelling MS data
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90 =============================================
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91
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92 **Positional arguments:**
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93
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94 input_path Path to datafile
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95 run_name Name of the current run
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96 format Format of generated file
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97
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98 **optional arguments:**
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99 -h, --help show this help message and exit
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100 --value Choices: "corrected_area", "isotopologue_fraction", "mean_enrichment". Select values to plot. This option can be given multiple times
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101
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102 -m METABOLITE Metabolite(s) to plot. For all, type in 'all'
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103 -c CONDITION Condition(s) to plot. For all, type in 'all'
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104 -t TIME Time(s) to plot. For all, type in 'all'
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105 -tp TEMPLATE_PATH Path to template file
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106
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107 -sa, --stacked_areaplot Create static stacked areaplot
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108 -bp, --barplot Create static barplot
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109 -mb, --meaned_barplot Create static barplot with meaned replicates
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110
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111 -IB, --interactive_barplot Create interactive stacked barplot
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112 -IM, --interactive_stacked_meanplot Create interactive stacked barplot with meaned replicates
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113 -IS, --interactive_areaplot Create interactive stacked areaplot
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114 -hm, --static_heatmap Create a static heatmap using mean enrichment data
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115 -cm, --static_clustermap Create a static heatmap with clustering using mean enrichment data
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116 -HM, --interactive_heatmap Create interactive heatmap using mean enrichment data
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117
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118 -s, --stack Add option if barplots should be unstacked
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119 -v, --verbose Turns logger to debug mode
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120 -a, --annot Add option if annotations should be added on maps
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121
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122 ]]></help>
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123 <citations>
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124 <citation type='bibtex'>
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125 @misc{githubisoplot,
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126 author = {Le Gregam, Loic},
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127 year = {2021},
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128 title = {isoplot},
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129 publisher = {GitHub},
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130 journal = {GitHub repository},
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131 url = {https://github.com/llegregam},
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132 }</citation>
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133 </citations>
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134 </tool> |
