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annotate velveth.xml @ 1:5da9a0e2fb2d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
author devteam
date Wed, 12 Feb 2020 11:16:32 -0500
parents 08256557922f
children 8d09f8be269e
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5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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1 <tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.1">
0
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2 <description>Prepare a dataset for the Velvet velvetg Assembler</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
1
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8 <version_command><![CDATA[
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9 velveth 2>&1 | grep "Version" | sed -e 's/Version //'
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10 ]]></version_command>
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11 <command><![CDATA[
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12 mkdir -p '${out_file1.extra_files_path}' &&
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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13 velveth
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14 '${out_file1.extra_files_path}'
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15 $hash_length
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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16 $strand_specific
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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17 #for $i in $inputs
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18 ${i.file_format}
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19 ${i.read_type}
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20 '${i.input}'
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21 #end for
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22 ]]></command>
0
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23 <inputs>
1
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24 <param name="hash_length" type="select" label="Hash length" help="k-mer length in base pairs of the words being hashed">
0
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25 <option value="11">11</option>
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26 <option value="13">13</option>
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27 <option value="15">15</option>
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28 <option value="17">17</option>
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29 <option value="19">19</option>
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30 <option value="21" selected="yes">21</option>
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31 <option value="23">23</option>
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32 <option value="25">25</option>
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33 <option value="27">27</option>
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34 <option value="29">29</option>
1
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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35 <option value="31">31</option>
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36 <option value="33">33</option>
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37 <option value="35">35</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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38 <option value="37">37</option>
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39 <option value="39">39</option>
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40 <option value="41">41</option>
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41 <option value="43">43</option>
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42 <option value="45">45</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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43 <option value="47">47</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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44 <option value="49">49</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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45 <option value="51">51</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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46 <option value="53">53</option>
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47 <option value="55">55</option>
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48 <option value="57">57</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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49 <option value="59">59</option>
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50 <option value="61">61</option>
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51 <option value="63">63</option>
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52 <option value="65">65</option>
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53 <option value="67">67</option>
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54 <option value="69">69</option>
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55 <option value="71">71</option>
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56 <option value="73">73</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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57 <option value="75">75</option>
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58 <option value="77">77</option>
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59 <option value="79">79</option>
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60 <option value="81">81</option>
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61 <option value="83">83</option>
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62 <option value="85">85</option>
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63 <option value="87">87</option>
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64 <option value="89">89</option>
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65 <option value="91">91</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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66 <option value="93">93</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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67 <option value="95">95</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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68 <option value="97">97</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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69 <option value="99">99</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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70 <option value="101">101</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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71 <option value="103">103</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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72 <option value="105">105</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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73 <option value="107">107</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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74 <option value="109">109</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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75 <option value="111">111</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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76 <option value="113">113</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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77 <option value="115">115</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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78 <option value="117">117</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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79 <option value="119">119</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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80 <option value="121">121</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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81 <option value="123">123</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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82 <option value="125">125</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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83 <option value="127">127</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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84 <option value="129">129</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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85 <option value="131">131</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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86 <option value="133">133</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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87 <option value="135">135</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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88 <option value="137">137</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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89 <option value="139">139</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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90 <option value="141">141</option>
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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91 <option value="143">143</option>
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92 <option value="145">145</option>
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93 <option value="147">147</option>
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94 <option value="149">149</option>
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95 <option value="151">151</option>
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96 <option value="153">153</option>
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97 <option value="155">155</option>
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98 <option value="157">157</option>
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99 <option value="159">159</option>
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100 <option value="161">161</option>
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101 <option value="163">163</option>
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102 <option value="165">165</option>
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103 <option value="167">167</option>
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104 <option value="169">169</option>
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105 <option value="171">171</option>
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106 <option value="173">173</option>
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107 <option value="175">175</option>
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108 <option value="177">177</option>
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109 <option value="179">179</option>
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110 <option value="181">181</option>
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111 <option value="183">183</option>
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112 <option value="185">185</option>
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113 <option value="187">187</option>
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114 <option value="189">189</option>
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115 <option value="191">191</option>
0
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116 </param>
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117 <param name="strand_specific" type="boolean" checked="false" truevalue="-strand_specific" falsevalue="" label="Use strand specific transcriptome sequencing" help="If you are using a strand specific transcriptome sequencing protocol, you may wish to use this option for better results."/>
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118 <repeat name="inputs" title="Input Files">
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119 <param label="file format" name="file_format" type="select">
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120 <option value="-fasta" selected="yes">fasta</option>
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121 <option value="-fastq">fastq</option>
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122 <option value="-eland">eland</option>
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123 <option value="-gerald">gerald</option>
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124 </param>
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125 <param label="read type" name="read_type" type="select">
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126 <option value="-short" selected="yes">short reads</option>
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127 <option value="-shortPaired">shortPaired reads</option>
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128 <option value="-short2">short2 reads</option>
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129 <option value="-shortPaired2">shortPaired2 reads</option>
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130 <option value="-long">long reads</option>
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131 <option value="-longPaired">longPaired reads</option>
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132 </param>
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133
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134 <param name="input" type="data" format="fasta,fastq,eland,gerald" label="Dataset"/>
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135 </repeat>
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136 </inputs>
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137 <outputs>
1
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138 <data name="out_file1" format="velvet" />
0
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139 </outputs>
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140 <tests>
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141 <test>
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142 <param name="hash_length" value="21" />
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143 <param name="read_type" value="-shortPaired" />
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144 <!-- <repeat name="inputs"> -->
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145 <param name="file_format" value="fasta" />
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146 <param name="read_type" value="shortPaired reads" />
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147 <param name="input" value="velvet_test_reads.fa" ftype="fasta" />
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148 <!-- </repeat> -->
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149 <param name="strand_specific" value="" />
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150 <output name="out_file1" file="velveth_test1/output.html" lines_diff="4">
1
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151 <extra_files type="file" name="Sequences" value="velveth_test1/Sequences" />
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152 <extra_files type="file" name="Roadmaps" value="velveth_test1/Roadmaps" />
0
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153 </output>
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154 </test>
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155 </tests>
1
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156 <help><![CDATA[
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157 **What it does**
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158
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159 Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
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160
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161 Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
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162
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163 Read the Velvet `documentation`__ for details on using the Velvet Assembler.
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164
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165 .. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
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166
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167 .. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
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168
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169 ------
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170
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171 **Velveth**
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172
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173 Velveth takes in a number of sequence files, produces a hashtable, then outputs two files in an output directory (creating it if necessary), Sequences and Roadmaps, which are necessary to velvetg.
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174
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175 ------
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176
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177 **Hash Length**
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178
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179 The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed.
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180
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181 The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints::
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182
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183 # it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.
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184 # it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits
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185 # it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.
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186
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187 Now you still have quite a lot of possibilities. As is often the case, it's a trade- off between specificity and sensitivity. Longer kmers bring you more specificity (i.e. less spurious overlaps) but lowers coverage (cf. below). . . so there's a sweet spot to be found with time and experience.
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188 We like to think in terms of "k-mer coverage", i.e. how many times has a k-mer been seen among the reads. The relation between k-mer coverage Ck and standard (nucleotide-wise) coverage C is Ck = C # (L - k + 1)/L where k is your hash length, and L you read length.
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189 Experience shows that this kmer coverage should be above 10 to start getting decent results. If Ck is above 20, you might be "wasting" coverage. Experience also shows that empirical tests with different values for k are not that costly to run!
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190
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191 **Input Files**
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192
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193 Velvet works mainly with fasta and fastq formats. For paired-end reads, the assumption is that each read is next to its mate
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194 read. In other words, if the reads are indexed from 0, then reads 0 and 1 are paired, 2 and 3, 4 and 5, etc.
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195
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196 Supported file formats are::
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197
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198 fasta
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199 fastq
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200 fasta.gz
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201 fastq.gz
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202 eland
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203 gerald
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204
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205 Read categories are::
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206
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207 short (default)
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208 shortPaired
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209 short2 (same as short, but for a separate insert-size library)
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210 shortPaired2 (see above)
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211 long (for Sanger, 454 or even reference sequences)
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212 longPaired
1
5da9a0e2fb2d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
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213 ]]></help>
0
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214 <expand macro="citation"/>
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215 </tool>