Mercurial > repos > bebatut > export2graphlan

annotate export2graphlan.xml @ 0:f3a11239c704 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
author bebatut
date Mon, 01 Feb 2016 07:45:45 -0500
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children f7e87cc38f57
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f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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1 <tool id="export2graphlan" name="Export to GraPhlAn" version="0.1.0">
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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2
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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3 <description></description>
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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4
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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5 <requirements>
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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6 <requirement type="package" version="0.16">pandas</requirement>
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7 <requirement type="package" version="0.16">scipy</requirement>
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8 <requirement type="package" version="1.4">matplotlib</requirement>
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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9 <requirement type="package" version="1.0">export2graphlan</requirement>
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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10 </requirements>
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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11
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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12 <stdio>
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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13 </stdio>
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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14
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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15 <version_command>
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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16 <![CDATA[
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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17 python \${EXPORT2GRAPHLAN_DIR}/export2graphlan.py -v
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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18 ]]>
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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19 </version_command>
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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21 <command>
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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22 <![CDATA[
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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23 python \${EXPORT2GRAPHLAN_DIR}/export2graphlan.py
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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24 -i $lefse_input
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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25
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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26 #if $lefse_output
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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27 -o lefse_output
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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28 #end if
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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29
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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30 -t $tree
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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31 -a $annotation
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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32
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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33 #if $annotations
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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34 --annotations $annotations
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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35 #end if
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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36
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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37 #if $external_annotations
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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38 --external_annotations $external_annotations
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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39 #end if
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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40
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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41 #if $background_levels
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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42 --background_levels $background_levels
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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43 #end if
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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44
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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45 #if $background_clades
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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46 --background_clades "$background_clades"
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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47 #end if
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48
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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49 #if $background_colors
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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50 --background_colors "$background_colors"
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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51 #end if
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52
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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53 #if $title
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54 --title "title"
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55 #end if
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56
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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57 --title_font_size $title_font_size
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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58 --def_clade_size $def_clade_size
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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59 --min_clade_size $min_clade_size
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60 --max_clade_size $max_clade_size
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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61 --def_font_size $def_font_size
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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62 --min_font_size $min_font_size
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63 --max_font_size $max_font_size
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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64 --annotation_legend_font_size $annotation_legend_font_size
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65 --abundance_threshold $abundance_threshold
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66
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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67 #if $most_abundant
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68 --most_abundant $most_abundant
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69 #end if
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70
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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71 #if $least_biomarkers
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72 --least_biomarkers $least_biomarkers
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73 #end if
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74
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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75 --fname_row $fname_row
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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76 --sname_row $sname_row
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77
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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78 #if $metadata_rows
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79 --metadata_rows $metadata_rows
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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80 #end if
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81
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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82 #if $skip_rows
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83 --skip_rows $skip_rows
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84 #end if
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85
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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86 #if $sperc
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87 --sperc $sperc
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88 #end if
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89
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90 #if $fperc
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91 --fperc $fperc
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92 #end if
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93
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94 #if $stop
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95 --stop $stop
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96 #end if
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97
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98 #if $ftop
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99 --ftop $ftop
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100 #end if
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101 ]]>
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102 </command>
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103
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104 <inputs>
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105 <param name="lefse_input" type="data" format="tabular" label="Input file"
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106 help="Identical to LEfSe input file (--lefse_input)"/>
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107
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108 <param name="lefse_output" type="data" format="tabular" label="Input file
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109 corresponding to LEfSe output file (Optional)" help="(--lefse_output)"
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110 optional="True"/>
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111
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112 <param name="annotations" type="text" label="List which levels should be
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113 annotated in the tree (Optional)" help="The levels must be in
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114 comma-separated form (--annotations)" optional="True"/>
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115
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116 <param name="external_annotations" type="text" label="List which levels
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117 should use the external legend for the annotation (Optional)"
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118 help="The levels must be in comma-separated form (--external_annotations)"
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119 optional="True"/>
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120
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121 <param name="background_levels" type="text" label="List which levels should
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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122 be highlight with a shaded background (Optional)"
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123 help="The levels must be in comma-separated form (--background_levels)"
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124 optional="True"/>
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125
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126 <param name="background_clades" type="text" label="List of the clades that
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127 should be highlight with a shaded background (Optional)"
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128 help="The clades must be in comma-separated form (--background_clades)"
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129 optional="True"/>
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130
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131 <param name="background_colors" type="text" label="List of color to use
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132 for the shaded background (Optional)"
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133 help="Colors can be either in RGB or HSV (using a semi-colon to
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134 separate values, surrounded with ()). The different colors must be
f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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135 in comma-separated form (--background_colors)"
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136 optional="True"/>
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137
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138 <param name="title" type="text" label="Title of the GraPhlAn plot (Optional)"
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139 help="(--title)" optional="True"/>
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140
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141 <param name="title_font_size" type="integer" value="15" label="Title
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142 font size" help="(--title_font_size)"/>
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143
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144 <param name="def_clade_size" type="integer" value="10" label="Default
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145 size for clades that are not found as biomarkers"
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146 help="(--def_clade_size)"/>
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147
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148 <param name="min_clade_size" type="integer" value="20" label="Minimum
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149 value of clades that are biomarkers" help="(--min_clade_size)"/>
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150
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151 <param name="max_clade_size" type="integer" value="200" label="Maximum
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152 value of clades that are biomarkers" help="(--max_clade_size)"/>
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153
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154 <param name="def_font_size" type="integer" value="10" label="Default
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155 font size" help="(--def_font_size)"/>
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156
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157 <param name="min_font_size" type="integer" value="8" label="Minimum
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158 font size" help="(--min_font_size)"/>
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159
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160 <param name="max_font_size" type="integer" value="12" label="Maximum
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161 font size" help="(--max_font_size)"/>
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162
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163 <param name="annotation_legend_font_size" type="integer" value="10"
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164 label="Font size for the annotation legend"
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165 help="(--annotation_legend_font_size)"/>
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166
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167 <param name="abundance_threshold" type="float" value="20.0"
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168 label="Minimun abundance value for a clade to be annotated"
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169 help="(--abundance_threshold)"/>
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170
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171 <param name="most_abundant" type="integer" label="Number of clades to
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172 highlight (Optional)" help="(--most_abundant)" optional="True"/>
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173
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174 <param name="least_biomarkers" type="integer" label="Minimum number of
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175 biomarkers to extract (Optional)" help=" The taxonomy is parsed, and
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176 the level is choosen in order to have at least the specified number
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177 of biomarkers(--least_biomarkers)" optional="True"/>
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178
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179 <param name="fname_row" type="integer" value="0" label="Row number
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180 containing the names of the features" help="-1 specifies that no
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181 names are present in the matrix (--fname_row)"/>
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182
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183 <param name="sname_row" type="integer" value="0" label="Row number
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184 containing the names of the samples" help="-1 specifies that no
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185 names are present in the matrix (--sname_row)"/>
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186
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187 <param name="metadata_rows" type="integer" label="Row number
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188 to use as metadata (Optional)" help="(--metadata_rows)" optional="True"/>
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189
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190 <param name="skip_rows" type="text" label="Row number to skip
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191 from the input file" help="The row numbers ar indexed to 0 and comma
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192 separated (--skip_rows)" optional="True"/>
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193
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194 <param name="sperc" type="float" label="Percentile of sample value
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195 distribution for sample selection (Optional)" help="(--sperc)"
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196 optional="True"/>
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197
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198 <param name="fperc" type="float" label="Percentile of feature value
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199 distribution for sample selection (Optional)" help="(--fperc)"
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200 optional="True"/>
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201
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202 <param name="stop" type="integer" label="Number of top samples to select
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203 (Optional)" help="The order is based on percentile specified by --sperc
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204 (--stop)" optional="True"/>
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205
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206 <param name="ftop" type="integer" label="Number of top features to select
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207 (Optional)" help="The order is based on percentile specified by --fperc
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208 (--ftop)" optional="True"/>
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209 </inputs>
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210
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211 <outputs>
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212 <data format="txt" name="tree"
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213 label="${tool.name} on ${on_string}: Tree" />
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214 <data format="txt" name="annotation"
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215 label="${tool.name} on ${on_string}: Annotation" />
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216
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217 </outputs>
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218
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219 <tests>
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220 <test>
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221 </test>
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222 </tests>
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223
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224 <help><![CDATA[
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225
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226 **What it does**
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227
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228 export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. For more information, check the
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229 `user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_.
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230
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231 ]]></help>
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232
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233 <citations>
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234 </citations>
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235 </tool>