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annotate das_tool.xml @ 0:a8e434ebe961 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
author iuc
date Mon, 27 Jun 2022 12:41:23 +0000
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0
a8e434ebe961 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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1 <tool id="das_tool" name="DAS Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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3 for genome resolved metagenomics
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="biotools"/>
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9 <expand macro="requirements"/>
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10 <expand macro="version"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #set $bins = ""
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13 #set $labels = ""
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14 #set $sep = ""
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15 #for $i, $s in enumerate($binning)
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16 #set $bins += "%s%s" %($sep, $s.bins)
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17 #set $labels += "%s%s" %($sep, $s.labels)
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18 #set $sep = ","
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19 #end for
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20
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21 #if $adv.proteins
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22 ln -s $adv.proteins 'proteins' &&
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23 #end if
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24
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25 DAS_Tool
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26 --contigs '$contigs'
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27 --outputbasename 'outputs'
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28 --bins '$bins'
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29 --labels '$labels'
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30 --search_engine '$adv.search_engine'
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31 #if $adv.proteins
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32 --proteins 'proteins'
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33 #end if
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34 --score_threshold $adv.score_threshold
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35 --duplicate_penalty $adv.duplicate_penalty
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36 --megabin_penalty $adv.megabin_penalty
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37 $output.write_bin_evals
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38 $output.write_bins.write_bins
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39 #if str($output.write_bins.write_bins) != ''
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40 $output.write_bins.write_unbinned
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41 #end if
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42 $output.debug
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43 --threads \${GALAXY_SLOTS:-1}
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44 ]]></command>
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45 <inputs>
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46 <param argument="--contigs" type="data" format="fasta" label="Contig sequences"/>
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47 <repeat name="binning" title="Bins" min="1">
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48 <param argument="--bins" type="data" format="tabular" label="Contigs-to-bin table" help="Tabular with two columns: contig-IDs and bin-IDs. Fasta_to_Contigs2Bin can be used to Converts genome bins in fasta format to Contigs-to-bin table"/>
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49 <param argument="--labels" type="text" value="" label="Name of binning prediction tool used to generate the table"/>
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50 </repeat>
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51 <section name="adv" title="Advanced options">
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52 <param argument="--search_engine" type="select" label="Engine used for single copy gene identification">
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53 <option value="diamond" selected="true">diamond</option>
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54 <option value="blastp">blastp</option>
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55 </param>
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56 <param argument="--proteins" type="data" format="fasta" optional="true" label="Predicted proteins" help="The file should be prodigal fasta format: >contigID_geneNo"/>
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57 <param argument="--score_threshold" type="float" min="0" max="1" value="0.5" label="Score threshold until selection algorithm will keep selecting bins"/>
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58 <param argument="--duplicate_penalty" type="float" min="0" max="3" value="0.6" label="Penalty for duplicate single copy genes per bin (weight b)" help="Only change if you know what you are doing"/>
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59 <param argument="--megabin_penalty" type="float" min="0" max="3" value="0.5" label="Penalty for megabins (weight c)" help="Only change if you know what you are doing"/>
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60 </section>
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61 <section name="output" title="Outputs">
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62 <param name="proteins" type="boolean" checked="false" label="Output predicted proteins?"/>
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63 <param argument="--write_bin_evals" type="boolean" truevalue="--write_bin_evals" falsevalue="" checked="false" label="Write evaluation of input bin sets?"/>
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64 <conditional name="write_bins">
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65 <param argument="--write_bins" type="select" label="Export bins as fasta files?">
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66 <option value="--write_bins" selected="true">Yes</option>
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67 <option value="">No</option>
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68 </param>
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69 <when value="--write_bins">
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70 <param argument="--write_unbinned" type="boolean" truevalue="--write_unbinned" falsevalue="" checked="false" label="Export unbinned contigs as fasta file?"/>
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71 </when>
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72 <when value=""/>
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73 </conditional>
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74 <param argument="--debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Write debug information to log file?"/>
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75 </section>
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76 </inputs>
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77 <outputs>
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78 <data name="summary" format="tabular" from_work_dir="outputs_DASTool_summary.tsv" label="${tool.name} on ${on_string}: Summary of output bins" />
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79 <data name="contigs2bin" format="tabular" from_work_dir="outputs_DASTool_contig2bin.tsv" label="${tool.name} on ${on_string}: Contigs to bin file for the output bins" />
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80 <data name="log" format="txt" from_work_dir="outputs_DASTool.log" label="${tool.name} on ${on_string}: Log" />
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81 <data name="eval" format="tabular" from_work_dir="outputs_allBins.eval" label="${tool.name} on ${on_string}: Quality and completeness estimates of input bin sets" >
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82 <filter>output['write_bin_evals']</filter>
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83 </data>
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84 <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
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85 <filter>output['write_bins']['write_bins'] != ""</filter>
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86 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fa" format="fasta" directory="outputs_DASTool_bins" />
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87 </collection>
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88 <data name="unbinned_contigs" format="fasta" from_work_dir="outputs_DASTool_bins/unbinned.fa" label="${tool.name} on ${on_string}: Unbinned contigs" >
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89 <filter>output['write_bins']['write_bins'] != "" and output['write_bins']['write_unbinned']</filter>
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90 </data>
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91 <data name="proteins" format="fasta" from_work_dir="outputs_proteins.faa" label="${tool.name} on ${on_string}: Proteins" >
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92 <filter>output['proteins']</filter>
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93 </data>
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94 </outputs>
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95 <tests>
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96 <test expect_num_outputs="4">
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97 <param name="contigs" value="contigs.fasta"/>
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98 <repeat name="binning">
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99 <param name="bins" value="metabat.tabular"/>
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100 <param name="labels" value="metabat"/>
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101 </repeat>
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102 <section name="adv">
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103 <param name="search_engine" value="diamond"/>
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104 <param name="proteins" value="proteins.fasta"/>
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105 <param name="score_threshold" value="0.5"/>
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106 <param name="duplicate_penalty" value="0.6"/>
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107 <param name="megabin_penalty" value="0.5" />
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108 </section>
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109 <section name="output">
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110 <param name="write_bin_evals" value="true"/>
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111 <conditional name="write_bins">
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112 <param name="write_bins" value=""/>
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113 </conditional>
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114 <param name="debug" value="true"/>
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115 </section>
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116 <output name="summary" ftype="tabular">
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117 <assert_contents>
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118 <has_text text="unique_SCGs"/>
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119 <has_text text="metabat.8"/>
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120 <has_text text="bacteria"/>
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121 </assert_contents>
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122 </output>
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123 <output name="contigs2bin" ftype="tabular">
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124 <assert_contents>
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125 <has_text text="Ley3_66761_scaffold_6"/>
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126 </assert_contents>
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127 </output>
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128 <output name="log" ftype="txt">
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129 <assert_contents>
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130 <has_text text="Skipping gene prediction"/>
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131 <has_text text="#Target sequences to report alignments for: 1"/>
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132 </assert_contents>
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133 </output>
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134 <output name="eval" ftype="tabular">
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135 <assert_contents>
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136 <has_text text="unique_SCGs"/>
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137 <has_text text="metabat.8"/>
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138 </assert_contents>
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139 </output>
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140 </test>
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141 <test expect_num_outputs="6">
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142 <param name="contigs" value="contigs.fasta"/>
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143 <repeat name="binning">
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144 <param name="bins" value="metabat.tabular"/>
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145 <param name="labels" value="metabat"/>
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146 </repeat>
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147 <section name="adv">
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148 <param name="search_engine" value="diamond"/>
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149 <param name="score_threshold" value="0.5"/>
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150 <param name="duplicate_penalty" value="0.6"/>
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151 <param name="megabin_penalty" value="0.5" />
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152 </section>
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153 <section name="output">
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154 <param name="proteins" value="true"/>
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155 <param name="write_bin_evals" value="false"/>
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156 <conditional name="write_bins">
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157 <param name="write_bins" value="--write_bins"/>
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158 <param name="write_unbinned" value="true"/>
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159 </conditional>
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160 <param name="debug" value="true"/>
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161 </section>
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162 <output name="summary" ftype="tabular">
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163 <assert_contents>
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164 <has_text text="unique_SCGs"/>
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165 <has_text text="metabat.8"/>
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166 <has_text text="bacteria"/>
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167 </assert_contents>
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168 </output>
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169 <output name="contigs2bin" ftype="tabular">
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170 <assert_contents>
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171 <has_text text="Ley3_66761_scaffold_6"/>
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172 </assert_contents>
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173 </output>
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174 <output name="log" ftype="txt">
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175 <assert_contents>
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176 <has_text text="Parameters"/>
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177 <has_text text="Predicting genes"/>
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178 </assert_contents>
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179 </output>
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180 <output_collection name="bins" count="1">
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181 <element name="8" ftype="fasta">
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182 <assert_contents>
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183 <has_text text=">Ley3_66761_scaffold_6"/>
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184 </assert_contents>
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185 </element>
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186 </output_collection>
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187 <output name="unbinned_contigs" ftype="fasta">
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188 <assert_contents>
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189 <has_text text=">Ley3_66761_scaffold_505"/>
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190 </assert_contents>
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191 </output>
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192 <output name="proteins" ftype="fasta">
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193 <assert_contents>
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194 <has_text text="Ley3_66761_scaffold_6_1 # 1 # 786 # 1 #"/>
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195 </assert_contents>
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196 </output>
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197 </test>
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198 </tests>
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199 <help><![CDATA[
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200 @HELP_HEADER@
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201
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202 Inputs
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203 ======
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204
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205 - Bins: Tab separated files of contig-IDs and bin-IDs. Contigs to bin file example: ::
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206
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207 Contig_1 bin.01
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208 Contig_8 bin.01
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209 Contig_42 bin.02
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210 Contig_49 bin.03
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211
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212 - Contigs: Assembled contigs in fasta format: ::
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213
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214 >Contig_1
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215 ATCATCGTCCGCATCGACGAATTCGGCGAACGAGTACCCCTGACCATCTCCGATTA...
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216 >Contig_2
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217 GATCGTCACGCAGGCTATCGGAGCCTCGACCCGCAAGCTCTGCGCCTTGGAGCAGG...
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218
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219 - [Optional] Proteins: Predicted proteins in prodigal fasta format. Header contains contig-ID and gene number: ::
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220
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221 >Contig_1_1
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222 MPRKNKKLPRHLLVIRTSAMGDVAMLPHALRALKEAYPEVKVTVATKSLFHPFFEG...
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223 >Contig_1_2
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224 MANKIPRVPVREQDPKVRATNFEEVCYGYNVEEATLEASRCLNCKNPRCVAACPVN...
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225
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226 Outputs
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227 =======
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228
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229 - Summary of output bins including quality and completeness estimates
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230 - Contigs to bin file of output bins
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231 - [Optional] Quality and completeness estimates of input bin sets
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232 - [Optional] Bins in fasta format
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233 - [Optional] Unbinned contigs
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234
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235 ]]></help>
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236 <expand macro="citations"/>
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237 </tool>