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comparison 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
comparison
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0:08256557922f 1:5da9a0e2fb2d
1 <tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.0"> 1 <tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.1">
2 <description>Prepare a dataset for the Velvet velvetg Assembler</description> 2 <description>Prepare a dataset for the Velvet velvetg Assembler</description>
3 <version_command>velveth 2&gt;&amp;1 | grep "Version" | sed -e 's/Version //'</version_command>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="requirements"/> 6 <expand macro="requirements"/>
8 <expand macro="stdio"/> 7 <expand macro="stdio"/>
9 <command interpreter="python"> 8 <version_command><![CDATA[
10 velveth_wrapper.py 9 velveth 2>&1 | grep "Version" | sed -e 's/Version //'
11 '$out_file1' '$out_file1.extra_files_path' 10 ]]></version_command>
12 $hash_length 11 <command><![CDATA[
13 $strand_specific 12 mkdir -p '${out_file1.extra_files_path}' &&
14 #for $i in $inputs 13 velveth
15 ${i.file_format} 14 '${out_file1.extra_files_path}'
16 ${i.read_type} 15 $hash_length
17 ${i.input} 16 $strand_specific
18 #end for 17 #for $i in $inputs
19 </command> 18 ${i.file_format}
19 ${i.read_type}
20 '${i.input}'
21 #end for
22 ]]></command>
20 <inputs> 23 <inputs>
21 <param label="Hash Length" name="hash_length" type="select" help="k-mer length in base pairs of the words being hashed."> 24 <param name="hash_length" type="select" label="Hash length" help="k-mer length in base pairs of the words being hashed">
22 <option value="11">11</option> 25 <option value="11">11</option>
23 <option value="13">13</option> 26 <option value="13">13</option>
24 <option value="15">15</option> 27 <option value="15">15</option>
25 <option value="17">17</option> 28 <option value="17">17</option>
26 <option value="19">19</option> 29 <option value="19">19</option>
27 <option value="21" selected="yes">21</option> 30 <option value="21" selected="yes">21</option>
28 <option value="23">23</option> 31 <option value="23">23</option>
29 <option value="25">25</option> 32 <option value="25">25</option>
30 <option value="27">27</option> 33 <option value="27">27</option>
31 <option value="29">29</option> 34 <option value="29">29</option>
35 <option value="31">31</option>
36 <option value="33">33</option>
37 <option value="35">35</option>
38 <option value="37">37</option>
39 <option value="39">39</option>
40 <option value="41">41</option>
41 <option value="43">43</option>
42 <option value="45">45</option>
43 <option value="47">47</option>
44 <option value="49">49</option>
45 <option value="51">51</option>
46 <option value="53">53</option>
47 <option value="55">55</option>
48 <option value="57">57</option>
49 <option value="59">59</option>
50 <option value="61">61</option>
51 <option value="63">63</option>
52 <option value="65">65</option>
53 <option value="67">67</option>
54 <option value="69">69</option>
55 <option value="71">71</option>
56 <option value="73">73</option>
57 <option value="75">75</option>
58 <option value="77">77</option>
59 <option value="79">79</option>
60 <option value="81">81</option>
61 <option value="83">83</option>
62 <option value="85">85</option>
63 <option value="87">87</option>
64 <option value="89">89</option>
65 <option value="91">91</option>
66 <option value="93">93</option>
67 <option value="95">95</option>
68 <option value="97">97</option>
69 <option value="99">99</option>
70 <option value="101">101</option>
71 <option value="103">103</option>
72 <option value="105">105</option>
73 <option value="107">107</option>
74 <option value="109">109</option>
75 <option value="111">111</option>
76 <option value="113">113</option>
77 <option value="115">115</option>
78 <option value="117">117</option>
79 <option value="119">119</option>
80 <option value="121">121</option>
81 <option value="123">123</option>
82 <option value="125">125</option>
83 <option value="127">127</option>
84 <option value="129">129</option>
85 <option value="131">131</option>
86 <option value="133">133</option>
87 <option value="135">135</option>
88 <option value="137">137</option>
89 <option value="139">139</option>
90 <option value="141">141</option>
91 <option value="143">143</option>
92 <option value="145">145</option>
93 <option value="147">147</option>
94 <option value="149">149</option>
95 <option value="151">151</option>
96 <option value="153">153</option>
97 <option value="155">155</option>
98 <option value="157">157</option>
99 <option value="159">159</option>
100 <option value="161">161</option>
101 <option value="163">163</option>
102 <option value="165">165</option>
103 <option value="167">167</option>
104 <option value="169">169</option>
105 <option value="171">171</option>
106 <option value="173">173</option>
107 <option value="175">175</option>
108 <option value="177">177</option>
109 <option value="179">179</option>
110 <option value="181">181</option>
111 <option value="183">183</option>
112 <option value="185">185</option>
113 <option value="187">187</option>
114 <option value="189">189</option>
115 <option value="191">191</option>
32 </param> 116 </param>
33 <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."/> 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."/>
34 <repeat name="inputs" title="Input Files"> 118 <repeat name="inputs" title="Input Files">
35 <param label="file format" name="file_format" type="select"> 119 <param label="file format" name="file_format" type="select">
36 <option value="-fasta" selected="yes">fasta</option> 120 <option value="-fasta" selected="yes">fasta</option>
49 133
50 <param name="input" type="data" format="fasta,fastq,eland,gerald" label="Dataset"/> 134 <param name="input" type="data" format="fasta,fastq,eland,gerald" label="Dataset"/>
51 </repeat> 135 </repeat>
52 </inputs> 136 </inputs>
53 <outputs> 137 <outputs>
54 <data format="velvet" name="out_file1" /> 138 <data name="out_file1" format="velvet" />
55 </outputs> 139 </outputs>
56 <requirements>
57 <requirement type="package">velvet</requirement>
58 </requirements>
59 <tests> 140 <tests>
60 <test> 141 <test>
61 <param name="hash_length" value="21" /> 142 <param name="hash_length" value="21" />
62 <param name="read_type" value="-shortPaired" /> 143 <param name="read_type" value="-shortPaired" />
63 <!-- <repeat name="inputs"> --> 144 <!-- <repeat name="inputs"> -->
65 <param name="read_type" value="shortPaired reads" /> 146 <param name="read_type" value="shortPaired reads" />
66 <param name="input" value="velvet_test_reads.fa" ftype="fasta" /> 147 <param name="input" value="velvet_test_reads.fa" ftype="fasta" />
67 <!-- </repeat> --> 148 <!-- </repeat> -->
68 <param name="strand_specific" value="" /> 149 <param name="strand_specific" value="" />
69 <output name="out_file1" file="velveth_test1/output.html" lines_diff="4"> 150 <output name="out_file1" file="velveth_test1/output.html" lines_diff="4">
70 <extra_files type="file" name='Sequences' value="velveth_test1/Sequences" compare="diff" /> 151 <extra_files type="file" name="Sequences" value="velveth_test1/Sequences" />
71 <extra_files type="file" name='Roadmaps' value="velveth_test1/Roadmaps" compare="diff" /> 152 <extra_files type="file" name="Roadmaps" value="velveth_test1/Roadmaps" />
72 </output> 153 </output>
73 </test> 154 </test>
74 </tests> 155 </tests>
75 <help> 156 <help><![CDATA[
76
77 **What it does** 157 **What it does**
78 158
79 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. 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.
80 160
81 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. 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.
128 shortPaired 208 shortPaired
129 short2 (same as short, but for a separate insert-size library) 209 short2 (same as short, but for a separate insert-size library)
130 shortPaired2 (see above) 210 shortPaired2 (see above)
131 long (for Sanger, 454 or even reference sequences) 211 long (for Sanger, 454 or even reference sequences)
132 longPaired 212 longPaired
133 213 ]]></help>
134 </help>
135 <expand macro="citation"/> 214 <expand macro="citation"/>
136 </tool> 215 </tool>