Mercurial > repos > jjohnson > contig_annotation_tool

annotate macros.xml @ 0:ad7507073c3f draft

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author jjohnson
date Sun, 24 Nov 2019 21:56:00 -0500
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children 9a01840eac52
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0
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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1 <macros>
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2 <token name="@VERSION@">5.0.3</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@">cat</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="version_command">
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10 <version_command>CAT --version</version_command>
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11 </xml>
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12 <token name="@DATABASE_FOLDER@">CAT_database</token>
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13 <token name="@TAXONOMY_FOLDER@">taxonomy</token>
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14 <xml name="cat_db">
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15 <conditional name="db">
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16 <param name="db_src" type="select" label="CAT database from">
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17 <option value="cached">local cached database</option>
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18 <option value="history">history</option>
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19 </param>
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20 <when value="cached">
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21 <param name="cat_builtin" type="select" label="Use a built-in CAT database" help="If the CAT database of interest is not listed, contact your Galaxy administrator">
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22 <options from_data_table="cat_databases">
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23 <filter type="sort_by" column="2" />
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24 <validator type="no_options" message="No CAT database is available." />
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25 </options>
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26 </param>
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27 </when>
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28 <when value="history">
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29 <param name="cat_db" type="data" format="txt" label="A history dataset from CAT prepare tool"/>
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30 </when>
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31 </conditional>
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32 </xml>
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33 <token name="@CAT_DB@"><![CDATA[
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34 #if $db.db_src == 'cached':
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35 --database_folder $db.cat_builtin.fields.database_folder
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36 --taxonomy_folder $db.cat_builtin.fields.taxonomy_folder
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37 #else
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38 #import os.path
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39 #set $catdb = $db.cat_db.extra_files_path
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40 --database_folder '$os.path.join($catdb,"@DATABASE_FOLDER@")'
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41 --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")'
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42 #end if
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43 ]]></token>
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44 <token name="@CAT_TAXONOMY@"><![CDATA[
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45 #if $db.db_src == 'cached':
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46 --taxonomy_folder $db.cat_builtin.fields.taxonomy_folder
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47 #else
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48 #import os.path
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49 #set $catdb = $db.cat_db.extra_files_path
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50 --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")'
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51 #end if
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52 ]]></token>
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53 <xml name="test_catdb">
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54 <conditional name="db">
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55 <param name="db_src" value="cached"/>
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56 <param name="cat_builtin" value="CAT_prepare_test"/>
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57 </conditional>
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58 </xml>
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59
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60 <xml name="use_intermediates">
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61 <conditional name="previous">
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62 <param name="use_previous" type="select" label="Use previous gene prediction and diamond alignment">
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63 <option value="no">No</option>
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64 <option value="yes">Yes</option>
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65 </param>
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66 <when value="no"/>
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67 <when value="yes">
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68 <param argument="--proteins_fasta" type="data" format="fasta" label="predicted proteins fasta"/>
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69 <param argument="--diamond_alignment" type="data" format="fasta" label="alignments file"/>
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70 </when>
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71 </conditional>
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72 </xml>
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73 <token name="@USE_INTERMEDIATES@"><![CDATA[
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74 #if $previous.use_previous == 'yes'
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75 --proteins_fasta '$previous.proteins_fasta'
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76 --diamond_alignment '$previous.diamond_alignment'
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77 #end if
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78 --out_prefix 'cat_output'
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79 ]]></token>
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80
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81 <xml name="custom_settings">
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82 <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/>
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83 <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/>
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84 </xml>
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85 <token name="@CUSTOM_SETTINGS@"><![CDATA[
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86 --range $range
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87 --fraction $fraction
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88 ]]></token>
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89 <xml name="add_names_options">
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90 <param argument="--only_official" type="boolean" truevalue="--only_official" falsevalue="" checked="true"
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91 label="Only output official level names."/>
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92 <param argument="--exclude_scores" type="boolean" truevalue="--exclude_scores" falsevalue="" checked="false"
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93 label="Exclude bit-score support scores in the lineage."/>
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94 </xml>
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95 <token name="@ADD_NAMES_OPTIONS@"><![CDATA[
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96 $only_official $exclude_scores
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97 ]]></token>
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98 <xml name="add_names">
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99 <conditional name="names">
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100 <param name="add_names" type="select" label="add_names">
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101 <option value="no">No</option>
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102 <option value="orf2lca">ORF2LCA.txt</option>
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103 <option value="classification">classification.txt</option>
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104 <option value="both">ORF2LCA.txt and classification.txt</option>
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105 </param>
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106 <when value="no"/>
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107 <when value="orf2lca">
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108 <expand macro="add_names_options"/>
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109 </when>
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110 <when value="classification">
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111 <expand macro="add_names_options"/>
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112 </when>
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113 <when value="both">
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114 <expand macro="add_names_options"/>
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115 </when>
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116 </conditional>
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117 </xml>
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118 <token name="@ADD_NAMES@"><![CDATA[
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119 #if $names.add_names in ['classification','both']:
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120 && CAT add_names $names.only_official $names.exclude_scores
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121 @CAT_TAXONOMY@
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122 #if $bcat == 'CAT'
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123 -i cat_output.contigs2classification.tsv
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124 #else
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125 -i cat_output.bin2classification.tsv
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126 #end if
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127 -o classification_names.txt
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128 && @TXT2TSV@ -i classification_names -o $classification_names
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129 #end if
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130 #if $names.add_names in ['orf2lca','both']:
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131 && CAT add_names $names.only_official $names.exclude_scores
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132 @CAT_TAXONOMY@
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133 -i cat_output.ORF2LCA.tsv
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134 -o orf2lca_names.txt
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135 && @TXT2TSV@ -i orf2lca_names.txt -o $orf2lca_names
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136 #end if
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137 ]]></token>
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138 <xml name="summarise">
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139 <param name="summarise" type="select" label="summarise">
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140 <option value="no">No</option>
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141 <option value="classification">classification.txt</option>
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142 </param>
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143 </xml>
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144 <token name="@SUMMARISE@"><![CDATA[
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145 #if $summarise in ['classification']:
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146 #if $names.add_names in ['classification','both'] and $names.only_official:
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147 #set $summary_input = $classification_names
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148 #else
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149 #set $summary_input = classification_offical_names
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150 && CAT add_names --only_official
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151 @CAT_TAXONOMY@
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152 #if $bcat == 'CAT'
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153 -i cat_output.contigs2classification.tsv
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154 #else
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155 -i cat_output.bin2classification.tsv
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156 #end if
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157 -o $summary_input
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158 #end if
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159 && CAT summarise
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160 #if $bcat == 'CAT'
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161 -c $contigs_fasta
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162 #end if
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163 -i $summary_input
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164 -o classification_summary.txt
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165 && @TXT2TSV@ -i classification_summary.txt -o $classification_summary
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166 #end if
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167 ]]></token>
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168
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169 <xml name="select_outputs">
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170 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">
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171 <option value="log" selected="true">CAT.log</option>
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172 <option value="predicted_proteins_faa" selected="true">predicted_proteins.faa</option>
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173 <option value="predicted_proteins_gff">predicted_proteins.gff</option>
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174 <option value="alignment_diamond">alignment.diamond</option>
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175 <option value="orf2lca" selected="true">ORF2LCA.txt</option>
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176 <yield/>
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177 </param>
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178 </xml>
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179 <xml name="select_cat_outputs">
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180 <param name="bcat" type="hidden" value="CAT"/>
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181 <param name="seqtype" type="hidden" value="contig"/>
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182 <expand macro="select_outputs">
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183 <option value="contig2classification" selected="true">contig2classification.txt</option>
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184 </expand>
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185 </xml>
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186 <xml name="select_bat_outputs">
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187 <param name="bcat" type="hidden" value="BAT"/>
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188 <param name="seqtype" type="hidden" value="bin"/>
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189 <expand macro="select_outputs">
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190 <option value="bin2classification" selected="true">bin2classification.txt</option>
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191 </expand>
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192 </xml>
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193
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194 <token name="@TXT2TSV@"><![CDATA[
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195 $__tool_directory__/tabpad.py
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196 ]]></token>
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197 <xml name="outputs">
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198 <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log">
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199 <filter>'log' in select_outputs or not select_outputs</filter>
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200 </data>
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201 <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa">
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202 <filter>'predicted_proteins_faa' in select_outputs</filter>
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203 </data>
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204 <data name="predicted_proteins_gff" format="gff" label="${bcat}.predicted_proteins.gff" from_work_dir="cat_output.predicted_proteins.gff">
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205 <filter>'predicted_proteins_gff' in select_outputs</filter>
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206 </data>
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207 <data name="alignment_diamond" format="tabular" label="${bcat}.alignment.diamond" from_work_dir="cat_output.alignment.diamond">
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208 <filter>'alignment_diamond' in select_outputs</filter>
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209 <actions>
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210 <action name="comment_lines" type="metadata" default="1" />
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211 <action name="column_names" type="metadata" default="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" />
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212 </actions>
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213 </data>
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214 <data name="orf2lca" format="tabular" label="${bcat}.ORF2LCA.txt" from_work_dir="cat_output.ORF2LCA.tsv">
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215 <filter>'orf2lca' in select_outputs</filter>
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216 <actions>
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217 <action name="comment_lines" type="metadata" default="1" />
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218 <action name="column_names" type="metadata" default="ORF,lineage,bit-score" />
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219 </actions>
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220 </data>
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221 <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv">
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222 <filter>'contig2classification' in select_outputs</filter>
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223 <actions>
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224 <action name="comment_lines" type="metadata" default="1" />
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225 <action name="column_names" type="metadata" default="contig,classification,reason,lineage,lineage scores" />
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226 </actions>
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227 </data>
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228 <data name="bin2classification" format="tabular" label="${bcat}.bin2classification.txt" from_work_dir="cat_output.bin2classification.tsv">
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229 <filter>'bin2classification' in select_outputs</filter>
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230 <actions>
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231 <action name="comment_lines" type="metadata" default="1" />
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232 <action name="column_names" type="metadata" default="bin,classification,reason,lineage,lineage scores" />
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233 </actions>
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234 </data>
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235 <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt">
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236 <filter>'orf2lca' in names.add_names</filter>
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237 <actions>
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238 <action name="comment_lines" type="metadata" default="1" />
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239 <action name="column_names" type="metadata" default="ORF,lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" />
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240 </actions>
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241 </data>
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242 <data name="classification_names" format="tabular" label="${bcat}.${seqtype}2classification.names.txt">
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243 <filter>'classification' in names.add_names</filter>
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244 <actions>
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245 <action name="comment_lines" type="metadata" default="1" />
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246 <action name="column_names" type="metadata" default="${seqtype},classification,reason,lineage,lineage scores,superkingdom,phylum,class,order,family,genus,species" />
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247 </actions>
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248 </data>
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249 <data name="classification_summary" format="tabular" label="${bcat}.${seqtype}2classification.summary.txt">
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250 <filter>'classification' in summarise</filter>
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251 <actions>
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252 <action name="comment_lines" type="metadata" default="1" />
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253 <action name="column_names" type="metadata" default="rank,clade,number of contigs,number of ORFs,number of positions" />
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254 </actions>
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255 </data>
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256 </xml>
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257 <token name="@COMMON_HELP@"><![CDATA[
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258 The CAT/BAT workflow is described at: https://github.com/dutilh/CAT
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259 ]]></token>
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260 <xml name="citations">
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261 <citations>
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262 <citation type="doi">https://doi.org/10.1101/072868</citation>
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263 <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation>
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264 <yield />
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265 </citations>
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266 </xml>
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267 </macros>