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annotate macros.xml @ 4:80ce9ca55697 draft

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planemo upload commit d27827cf38d30b9c98923f73bc9cae4ffe41361b
author galaxyp
date Fri, 07 Dec 2018 13:43:06 -0500
parents 47bfbd6597d0
children
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1 <macros>
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2 <token name="@VERSION@">0.99.2</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@VERSION@">metaquantome</requirement>
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6 <yield/>
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7 </requirements>
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8 </xml>
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9 <xml name="ONTOLOGY_ARGS">
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10 <conditional name="ontology_args">
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11 <param name="ontology" type="select" label="Ontology">
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12 <option value="go">Gene Ontology (GO terms)</option>
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13 <option value="ec">Enzyme Commission (EC) numbers</option>
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14 <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
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15 </param>
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16 <when value="go">
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17 <param argument="--slim_down" type="boolean" label="Use slim GO"/>
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18 </when>
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19 <when value="ec">
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20 <!-- do nothing -->
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21 </when>
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22 <when value="cog">
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23 <!-- do nothing -->
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24 </when>
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25 </conditional>
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26 </xml>
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27 <xml name="FUNC_FILE">
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28 <param argument="--func_file" type="data" format="tabular" label="Functional file"
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29 help="Tabular file with a peptide sequence column and a functional assignment column for GO-term, EC number, or COG."/>
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30 <param argument="--pep_colname_func" type="text" label="Peptide column name"
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31 help="The column name within the function file that corresponds to the peptide sequences">
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32 <validator type="empty_field"/>
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33 </param>
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34 <param argument="--func_colname" type="text" label="Functional column name"
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35 help="The column name within the function file with the functional terms">
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36 <validator type="empty_field"/>
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37 </param>
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38 </xml>
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39 <xml name="TAX_FILE">
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40 <param argument="--tax_file" type="data" format="tabular" label="Taxonomy assignments file"/>
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41 <param argument="--pep_colname_tax" type="text" label="Peptide column name"
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42 help="The column name within the taxonomy file that corresponds to the peptide sequences">
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43 <validator type="empty_field"/>
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44 </param>
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45 <param argument="--tax_colname" type="text" label="Taxonomy column name">
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46 <help>
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47 Name of taxonomy column in taxonomy assignments file. The column must
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48 be either NCBI taxids (strongly preferred) or taxonomy
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49 names. Unipept name output is known to function well,
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50 but other formats may not work.
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51 </help>
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52 <validator type="empty_field"/>
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53 </param>
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54 </xml>
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55 <token name="@MAKE_SAMPS_TSV@"><![CDATA[
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56 ### make samps config file
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57 #if $samps_args.samps_src == 'history':
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58 cat '$samps_args.samps_file' > samp_file.tab &&
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59 #else:
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60 #set $samp_header = 'group\tcolnames'
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61 echo -e '${samp_header}' > samp_file.tab &&
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62 #for $s in $samps_args.samps
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63 #set $sample = str($s.group_name) + '\t' + str($s.col_names)
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64 echo -e '${sample}' >> samp_file.tab &&
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65 #end for
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66 #end if
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67 ]]>
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68 </token>
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69 <token name="@DB_DIR@"><![CDATA[
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70 #if $db_dir.db_loc == 'auto':
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71 #if $mode_args.mode == 'ft'
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72 --ft_func_data_dir data
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73 --ft_tax_data_dir data
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74 #else
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75 --data_dir data
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76 #end if
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77 ## #elif $db_dir.db_loc == 'cached':
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78 #end if
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79 ]]>
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80 </token>
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81 <xml name="data_dir">
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82 <conditional name="db_dir">
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83 <param argument="db_loc" type="select" label="Taxonomy and Functional Databases">
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84 <option value="auto">automatically load databases</option>
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85 <!-- bioconda recipe would need to install the databases
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86 <option value="pkg">use default metaquantome databases (not current)</option>
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87 -->
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88 <!-- requires a data_manager
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89 <option value="cached">Use cached databases</option>
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90 -->
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91 </param>
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92 <when value="auto"/>
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93 <!-- bioconda recipe would need to install the databases
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94 <when value="pkg"/>
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95 -->
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96 <!-- requires a data_manager
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97 <when value="cached">
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98 </when>
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99 -->
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100 </conditional>
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101 </xml>
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102 <token name="@COMMON_PARAMS@"><![CDATA[
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103 --samps samp_file.tab
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104 --mode '$mode_args.mode'
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105 #if $mode_args.mode == 'f'
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106 --ontology='$mode_args.ontology_args.ontology'
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107 #if $mode_args.ontology_args.ontology == 'go'
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108 #if $mode_args.ontology_args.slim_down
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109 --slim_down
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110 #end if
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111 #end if
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112 #end if
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113 #if $mode_args.mode == 'ft'
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114 --ontology='$mode_args.ontology_args.ontology'
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115 #if $mode_args.ontology_args.ontology == 'go'
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116 #if $mode_args.ontology_args.slim_down
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117 --slim_down
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118 #end if
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119 #end if
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120 #end if
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121 ]]>
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122 </token>
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123 <token name="@EXPAND_PARAMS@"><![CDATA[
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124 --samps samp_file.tab
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125 --mode '$mode_args.mode'
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126 #if $mode_args.mode == 'f'
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127 --func_file='$mode_args.func_file'
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128 --func_colname='$mode_args.func_colname'
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129 --pep_colname_func='$mode_args.pep_colname_func'
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130 --ontology='$mode_args.ontology_args.ontology'
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131 #if $mode_args.ontology_args.ontology == 'go'
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132 #if $mode_args.ontology_args.slim_down
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133 --slim_down
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134 #end if
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135 #end if
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136 #end if
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137 #if $mode_args.mode =='t'
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138 --tax_file='$mode_args.tax_file'
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139 --tax_colname='$mode_args.tax_colname'
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140 --pep_colname_tax='$mode_args.pep_colname_tax'
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141 #end if
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142 #if $mode_args.mode == 'ft'
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143 --func_file='$mode_args.func_file'
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144 --func_colname='$mode_args.func_colname'
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145 --pep_colname_func='$mode_args.pep_colname_func'
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146 --ontology='$mode_args.ontology_args.ontology'
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147 #if $mode_args.ontology_args.ontology == 'go'
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148 #if $mode_args.ontology_args.slim_down
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149 --slim_down
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150 #end if
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151 #end if
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152 --tax_file='$mode_args.tax_file'
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153 --tax_colname='$mode_args.tax_colname'
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154 --pep_colname_tax='$mode_args.pep_colname_tax'
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155 --ft_tar_rank='$mode_args.ft_tar_rank'
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156 #end if
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157 ]]>
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158 </token>
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159
0
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160 <xml name="SAMPS">
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161 <conditional name="samps_args">
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162 <param argument="samps_src" type="select" label="Samples">
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163 <option value="history">Use a samples dataset from your history</option>
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164 <option value="build">Specify samples</option>
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165 </param>
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166 <when value="history">
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167 <param name="samps_file" type="data" format="tabular" label="Samples file">
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168 </param>
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169 </when>
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170 <when value="build">
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171 <repeat name="samps" title="Samples">
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172 <param name="group_name" type="text" label="Group name"/>
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173 <param name="col_names" type="text" label="Column names of samples in group"/>
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174 </repeat>
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175 </when>
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176 </conditional>
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177 </xml>
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178 <xml name="common_params">
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179 <conditional name="mode_args">
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180 <param argument="--mode" type="select" label="Mode">
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181 <option value="f">Functional analysis</option>
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182 <option value="t">Taxonomic analysis</option>
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183 <option value="ft">Functional-taxonomic interaction analysis</option>
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184 </param>
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185 <when value="f">
1
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186 <expand macro="ONTOLOGY_ARGS"/>
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187 </when>
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188 <when value="t">
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189 </when>
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190 <when value="ft">
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191 <expand macro="ONTOLOGY_ARGS"/>
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192 </when>
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193 </conditional>
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194 <expand macro="SAMPS"/>
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195 </xml>
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196 <xml name="expand_params">
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197 <conditional name="mode_args">
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198 <param argument="--mode" type="select" label="Mode">
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199 <option value="f">Functional analysis</option>
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200 <option value="t">Taxonomic analysis</option>
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201 <option value="ft">Functional-taxonomic interaction analysis</option>
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202 </param>
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203 <when value="f">
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204 <expand macro="FUNC_FILE"/>
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205 <expand macro="ONTOLOGY_ARGS"/>
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206 </when>
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207 <when value="t">
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208 <expand macro="TAX_FILE"/>
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209 </when>
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210 <when value="ft">
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211 <expand macro="FUNC_FILE"/>
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212 <expand macro="ONTOLOGY_ARGS"/>
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213 <expand macro="TAX_FILE"/>
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214 <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy">
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215 <option value="species">species</option>
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216 <option value="genus" selected="true">genus</option>
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217 <option value="family">family</option>
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218 <option value="order">order</option>
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219 <option value="class">class</option>
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220 <option value="phylum">phylum</option>
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221 <option value="kingdom">kingdom</option>
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222 </param>
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223 </when>
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224 </conditional>
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225 <expand macro="SAMPS"/>
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226 </xml>
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227
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228 <xml name="output_samples_choice">
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229 <param name="output_samps" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output the samples fiile"/>
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230 </xml>
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231 <xml name="output_samples">
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232 <data format="tabular" name="samples_file" label="${tool.name} on ${on_string} samples" from_work_dir="samp_file.tab">
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233 <filter>output_samps == True</filter>
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234 </data>
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235 </xml>
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236
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237 <xml name="citations">
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238 <citations>
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239 <yield />
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240 </citations>
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241 </xml>
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242 </macros>