Mercurial > repos > bebatut > export2graphlan

annotate export2graphlan.xml @ 4:4a3676d020e7 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit 1b95965e1a861ec37867be554e324eb5bc1ece82-dirty
author bebatut
date Wed, 20 Apr 2016 06:08:58 -0400
parents 953621231a6c
children f05bc567f1a5
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4a3676d020e7 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit 1b95965e1a861ec37867be554e324eb5bc1ece82-dirty
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1 <tool id="export2graphlan" name="Export to GraPhlAn" version="0.19">
0
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3 <description></description>
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5 <requirements>
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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>
4
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9 <requirement type="package" version="0.19">export2graphlan</requirement>
0
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10 </requirements>
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12 <stdio>
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13 </stdio>
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15 <version_command>
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16 <![CDATA[
3
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17 export2graphlan.py -v
0
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18 ]]>
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19 </version_command>
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21 <command>
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22 <![CDATA[
3
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23 export2graphlan.py
0
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24 -i $lefse_input
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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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26 #if $lefse_output
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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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f3a11239c704 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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30 -t $tree
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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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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
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35 #end if
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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
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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
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44
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45 #if $background_clades
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46 --background_clades "$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
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49 #if $background_colors
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50 --background_colors "$background_colors"
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51 #end if
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52
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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
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58 --def_clade_size $def_clade_size
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59 --min_clade_size $min_clade_size
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60 --max_clade_size $max_clade_size
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61 --def_font_size $def_font_size
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62 --min_font_size $min_font_size
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63 --max_font_size $max_font_size
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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
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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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71 #if $least_biomarkers
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72 --least_biomarkers $least_biomarkers
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73 #end if
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75 --fname_row $fname_row
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76 --sname_row $sname_row
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78 #if $metadata_rows
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79 --metadata_rows $metadata_rows
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80 #end if
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81
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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
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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>
1
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105 <param name="lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file (--lefse_input)"/>
0
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106
1
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107 <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file (Optional)" help="(--lefse_output)" optional="True"/>
0
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108
1
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109 <param name="annotations" type="text" label="List which levels should be annotated in the tree (Optional)" help="The levels must be in comma-separated form (--annotations)" optional="True"/>
0
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110
1
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111 <param name="external_annotations" type="text" label="List which levels should use the external legend for the annotation (Optional)" help="The levels must be in comma-separated form (--external_annotations)" optional="True"/>
0
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112
1
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113 <param name="background_levels" type="text" label="List which levels should be highlight with a shaded background (Optional)" help="The levels must be in comma-separated form (--background_levels)" optional="True"/>
0
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114
1
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115 <param name="background_clades" type="text" label="List of the clades that should be highlight with a shaded background (Optional)" help="The clades must be in comma-separated form (--background_clades)" optional="True"/>
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116
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117 <param name="background_colors" type="text" label="List of color to use for the shaded background (Optional)" help="Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()). The different colors must be in comma-separated form (--background_colors)" optional="True"/>
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118
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119 <param name="title" type="text" label="Title of the GraPhlAn plot (Optional)" help="(--title)" optional="True"/>
0
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120
1
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121 <param name="title_font_size" type="integer" value="15" label="Title font size" help="(--title_font_size)"/>
0
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122
1
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123 <param name="def_clade_size" type="integer" value="10" label="Default size for clades that are not found as biomarkers" help="(--def_clade_size)"/>
0
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124
1
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125 <param name="min_clade_size" type="integer" value="20" label="Minimum value of clades that are biomarkers" help="(--min_clade_size)"/>
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126
1
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127 <param name="max_clade_size" type="integer" value="200" label="Maximum value of clades that are biomarkers" help="(--max_clade_size)"/>
0
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128
1
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129 <param name="def_font_size" type="integer" value="10" label="Default font size" help="(--def_font_size)"/>
0
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130
1
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131 <param name="min_font_size" type="integer" value="8" label="Minimum font size" help="(--min_font_size)"/>
0
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132
1
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133 <param name="max_font_size" type="integer" value="12" label="Maximum font size" help="(--max_font_size)"/>
0
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134
1
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135 <param name="annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend" help="(--annotation_legend_font_size)"/>
0
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136
1
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137 <param name="abundance_threshold" type="float" value="20.0" label="Minimun abundance value for a clade to be annotated" help="(--abundance_threshold)"/>
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138
1
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139 <param name="most_abundant" type="integer" label="Number of clades to highlight (Optional)" help="(--most_abundant)" optional="True"/>
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140
1
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141 <param name="least_biomarkers" type="integer" label="Minimum number of biomarkers to extract (Optional)" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers(--least_biomarkers)" optional="True"/>
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142
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143 <param name="fname_row" type="integer" value="0" label="Row number containing the names of the features" help="-1 specifies that no names are present in the matrix (--fname_row)"/>
0
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144
1
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145 <param name="sname_row" type="integer" value="0" label="Row number containing the names of the samples" help="-1 specifies that no names are present in the matrix (--sname_row)"/>
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146
1
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147 <param name="metadata_rows" type="integer" label="Row number to use as metadata (Optional)" help="(--metadata_rows)" optional="True"/>
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148
1
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149 <param name="skip_rows" type="text" label="Row number to skip from the input file" help="The row numbers ar indexed to 0 and comma separated (--skip_rows)" optional="True"/>
0
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150
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151 <param name="sperc" type="float" label="Percentile of sample value
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152 distribution for sample selection (Optional)" help="(--sperc)"
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153 optional="True"/>
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154
1
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155 <param name="fperc" type="float" label="Percentile of feature value distribution for sample selection (Optional)" help="(--fperc)" optional="True"/>
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156
1
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157 <param name="stop" type="integer" label="Number of top samples to select (Optional)" help="The order is based on percentile specified by --sperc (--stop)" optional="True"/>
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158
1
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159 <param name="ftop" type="integer" label="Number of top features to select (Optional)" help="The order is based on percentile specified by --fperc (--ftop)" optional="True"/>
0
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160 </inputs>
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161
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162 <outputs>
1
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163 <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" />
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164 <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" />
0
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165 </outputs>
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166
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167 <tests>
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168 <test>
3
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169 <param name="lefse_input" value="input_profile.tabular"/>
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170 <param name="annotations" value=""/>
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171 <param name="external_annotations" value=""/>
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172 <param name="background_levels" value=""/>
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173 <param name="background_clades" value=""/>
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174 <param name="background_colors" value=""/>
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175 <param name="title" value=""/>
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176 <param name="title_font_size" value="15"/>
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177 <param name="def_clade_size" value="10"/>
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178 <param name="min_clade_size" value="20"/>
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179 <param name="max_clade_size" value="200"/>
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180 <param name="def_font_size" value="10"/>
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181 <param name="min_font_size" value="8"/>
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182 <param name="max_font_size" value="12"/>
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183 <param name="annotation_legend_font_size" value="10"/>
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184 <param name="abundance_threshold" value="20.0"/>
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185 <param name="most_abundant" value=""/>
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186 <param name="least_biomarkers" value=""/>
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187 <param name="fname_row" value="0"/>
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188 <param name="sname_row" value="0" />
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189 <param name="metadata_rows" value=""/>
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190 <param name="skip_rows" value=""/>
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191 <param name="sperc" value=""/>
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192 <param name="fperc" value=""/>
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193 <param name="stop" value=""/>
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194 <param name="ftop" value=""/>
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195 <output name="annotation" file="annotation_output.txt"/>
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196 <output name="tree" file="tree_output.txt"/>
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197 </test>
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198 </tests>
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199
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200 <help><![CDATA[
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201
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202 **What it does**
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203
4
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204 export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. It can convert MetaPhlAn, LEfSe, and/or HUMAnN output to GraPhlAn input format
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205
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206 In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.
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207
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208 For more information, check the
0
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209 `user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_.
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210
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211 ]]></help>
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212
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213 <citations>
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214 </citations>
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215 </tool>