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1 <macros>
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2 <token name="@plot_need_qa_headtoken@">
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3 </token>
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4 <xml name="plot_need_qa_outmacro">
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5 </xml>
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6 <token name="@plot_need_qa_token@">
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7 '$out_folder.extra_files_path'
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8 </token>
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9 <xml name="plot_need_qa_macro">
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10 <param name="out_folder" type="data" format="tabular" label="output of qa command" />
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11 </xml>
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12 <token name="@plot_headtoken@">
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13 mkdir bin_folder &&
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14 #for $k, $f in enumerate($bin_folder)
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15 #if $f
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16 ln -s "${f}" bin_folder\/${k}.fna &&
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17 #end if
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18 #end for &&
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19
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20 mkdir plot_folder &&
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21
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22 </token>
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23 <xml name="plot_outmacro">
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24 <collection name="plot_folder" type="list" label="${tool.name} on ${on_string} (plots)">
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25 <discover_datasets pattern="__name_and_ext__" directory="plot_folder" />
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26 </collection>
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27 </xml>
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28 <token name="@plot_token@">
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29 bin_folder
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30 plot_folder
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31 #if $image_type and $image_type is not None:
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32 --image_type $image_type
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33 #end if
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34 #if $dpi and $dpi is not None:
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35 --dpi $dpi
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36 #end if
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37 #if $font_size and $font_size is not None:
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38 --font_size $font_size
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39 #end if
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40 </token>
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41 <xml name="plot_macro">
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42 <param name="bin_folder" type="data" label="bins" multiple="true" format="fasta"/>
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43
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44 <param argument="--image_type" label="desired image type" name="image_type" optional="true" type="select">
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45 <option value="eps">eps</option>
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46 <option value="pdf">pdf</option>
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47 <option selected="true" value="png">png</option>
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48 <option value="ps">ps</option>
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49 <option value="svg">svg</option>
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50 </param>
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51 <param argument="--dpi" label="desired DPI of output image" name="dpi" optional="true" type="integer" value="600"/>
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52 <param argument="--font_size" label="Desired font size" name="font_size" optional="true" type="integer" value="8"/>
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53 </xml>
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54 <token name="@plot_single_headtoken@">
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55 </token>
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56 <xml name="plot_single_outmacro">
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57 </xml>
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58 <token name="@plot_single_token@">
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59 #if $width and $width is not None:
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60 --width $width
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61 #end if
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62 #if $height and $height is not None:
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63 --height $height
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64 #end if
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65 </token>
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66 <xml name="plot_single_macro">
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67 <param argument="--width" label="width of output image" name="width" optional="true" type="float" value="6.5"/>
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68 <param argument="--height" label="height of output image" name="height" optional="true" type="float" value="6.5"/>
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69 </xml>
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70 <token name="@plot_double_headtoken@">
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71 </token>
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72 <xml name="plot_double_outmacro">
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73 </xml>
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74 <token name="@plot_double_token@">
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75 #if $width and $width is not None:
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76 --width $width
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77 #end if
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78 #if $height and $height is not None:
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79 --height $height
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80 #end if
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81 </token>
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82 <xml name="plot_double_macro">
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83 <param argument="--width" label="width of output image" name="width" optional="true" type="float" value="6.5"/>
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84 <param argument="--height" label="height of output image" name="height" optional="true" type="float" value="3.5"/>
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85 </xml>
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86 <token name="@plot_rows_headtoken@">
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87 </token>
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88 <xml name="plot_rows_outmacro">
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89 </xml>
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90 <token name="@plot_rows_token@">
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91 #if $width and $width is not None:
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92 --width $width
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93 #end if
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94 #if $row_height and $row_height is not None:
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95 --row_height $row_height
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96 #end if
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97 </token>
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98 <xml name="plot_rows_macro">
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99 <param argument="--width" label="width of output image" name="width" optional="true" type="float" value="6.5"/>
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100 <param argument="--row_height" label="height of each row in the output image" name="row_height" optional="true" type="float" value="0.3"/>
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101 </xml>
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102 </macros>
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