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comparison velveth.xml @ 2:8d09f8be269e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
author iuc
date Tue, 16 Jun 2020 12:58:20 -0400
parents 5da9a0e2fb2d
children 920677cd220f
comparison
equal deleted inserted replaced
1:5da9a0e2fb2d 2:8d09f8be269e
1 <tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.1"> 1 <tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.2">
2 <description>Prepare a dataset for the Velvet velvetg Assembler</description> 2 <description>Prepare a dataset for the Velvet velvetg Assembler</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <version_command><![CDATA[ 8 <version_command><![CDATA[
9 velveth 2>&1 | grep "Version" | sed -e 's/Version //' 9 velveth 2>&1 | grep "Version" | sed -e 's/Version //'
10 ]]></version_command> 10 ]]></version_command>
11 <command><![CDATA[ 11 <command><![CDATA[
12 mkdir -p '${out_file1.extra_files_path}' && 12 export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" &&
13 velveth 13 mkdir -p '${outfile.extra_files_path}' &&
14 '${out_file1.extra_files_path}' 14 velveth
15 $hash_length 15 '$outfile.extra_files_path'
16 $strand_specific 16 $hash_length
17 #for $i in $inputs 17 #for $i in $inputs
18 ${i.file_format} 18 -${i.input_type.input.ext}
19 ${i.read_type} 19 ${i.input_type.read_type}
20 '${i.input}' 20 #if str( $i.input_type.input_type_selector ) == "paireds":
21 #end for 21 -separate '${i.input_type.input}' '${i.input_type.input2}'
22 #else if str( $i.input_type.input_type_selector ) == "pairedi":
23 -interleaved '${i.input_type.input}'
24 #else:
25 '${i.input_type.input}'
26 #end if
27 #end for
28 $strand_specific
22 ]]></command> 29 ]]></command>
23 <inputs> 30 <inputs>
24 <param name="hash_length" type="select" label="Hash length" help="k-mer length in base pairs of the words being hashed"> 31 <param label="Hash Length" name="hash_length" type="integer" value="21" min="11" max="191" help="k-mer length in base pairs of the words being hashed."/>
25 <option value="11">11</option>
26 <option value="13">13</option>
27 <option value="15">15</option>
28 <option value="17">17</option>
29 <option value="19">19</option>
30 <option value="21" selected="yes">21</option>
31 <option value="23">23</option>
32 <option value="25">25</option>
33 <option value="27">27</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>
116 </param>
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."/> 32 <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."/>
118 <repeat name="inputs" title="Input Files"> 33 <repeat name="inputs" title="Input Files">
119 <param label="file format" name="file_format" type="select"> 34 <conditional name="input_type">
120 <option value="-fasta" selected="yes">fasta</option> 35 <param name="input_type_selector" type="select" label="Choose the input type">
121 <option value="-fastq">fastq</option> 36 <option value="single" selected="true">Single ended</option>
122 <option value="-eland">eland</option> 37 <option value="paireds">separate paired end</option>
123 <option value="-gerald">gerald</option> 38 <option value="pairedi">interleaved paired end</option>
124 </param> 39 </param>
125 <param label="read type" name="read_type" type="select"> 40 <when value="single">
126 <option value="-short" selected="yes">short reads</option> 41 <param label="read type" name="read_type" type="select">
127 <option value="-shortPaired">shortPaired reads</option> 42 <option value="-short" selected="true">short reads</option>
128 <option value="-short2">short2 reads</option> 43 <option value="-short2">short2 reads</option>
129 <option value="-shortPaired2">shortPaired2 reads</option> 44 <option value="-short3">short3 reads</option>
130 <option value="-long">long reads</option> 45 <option value="-short4">short4 reads</option>
131 <option value="-longPaired">longPaired reads</option> 46 <option value="-long">long reads</option>
132 </param> 47 </param>
133 48 <param name="input" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Dataset"/>
134 <param name="input" type="data" format="fasta,fastq,eland,gerald" label="Dataset"/> 49 </when>
50 <when value="paireds">
51 <param label="read type" name="read_type" type="select" >
52 <option value="-shortPaired" selected="true">shortPaired reads</option>
53 <option value="-shortPaired2">shortPaired2 reads</option>
54 <option value="-shortPaired3">shortPaired3 reads</option>
55 <option value="-shortPaired4">shortPaired4 reads</option>
56 <option value="-longPaired">longPaired reads</option>
57 </param>
58 <param name="input" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Dataset"/>
59 <param name="input2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Dataset"/>
60 </when>
61 <when value="pairedi">
62 <param label="read type" name="read_type" type="select">
63 <option value="-shortPaired" selected="true">shortPaired reads</option>
64 <option value="-shortPaired2">shortPaired2 reads</option>
65 <option value="-shortPaired3">shortPaired3 reads</option>
66 <option value="-shortPaired4">shortPaired4 reads</option>
67 <option value="-longPaired">longPaired reads</option>
68 </param>
69 <param name="input" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Dataset"/>
70 </when>
71 </conditional>
135 </repeat> 72 </repeat>
136 </inputs> 73 </inputs>
137 <outputs> 74 <outputs>
138 <data name="out_file1" format="velvet" /> 75 <data format="velvet" name="outfile" />
139 </outputs> 76 </outputs>
140 <tests> 77 <tests>
141 <test> 78 <test>
142 <param name="hash_length" value="21" /> 79 <param name="hash_length" value="21" />
143 <param name="read_type" value="-shortPaired" /> 80 <repeat name="inputs">
144 <!-- <repeat name="inputs"> --> 81 <conditional name="input_type">
145 <param name="file_format" value="fasta" /> 82 <param name="input_type_selector" value="paireds" />
146 <param name="read_type" value="shortPaired reads" /> 83 <param name="read_type" value="-shortPaired" />
147 <param name="input" value="velvet_test_reads.fa" ftype="fasta" /> 84 <param name="input1" value="R1.fastq" ftype="fastq" />
148 <!-- </repeat> --> 85 <param name="input2" value="R2.fastq" ftype="fastq" />
86 </conditional>
87 </repeat>
149 <param name="strand_specific" value="" /> 88 <param name="strand_specific" value="" />
150 <output name="out_file1" file="velveth_test1/output.html" lines_diff="4"> 89 <output name="outfile" file="velveth_paireds.out">
151 <extra_files type="file" name="Sequences" value="velveth_test1/Sequences" /> 90 <extra_files type="file" name='Sequences' value="velveth_paireds/Sequences" compare="diff" />
152 <extra_files type="file" name="Roadmaps" value="velveth_test1/Roadmaps" /> 91 <extra_files type="file" name='Roadmaps' value="velveth_paireds/Roadmaps" compare="diff" />
92 </output>
93 </test>
94 <test>
95 <param name="hash_length" value="21" />
96 <repeat name="inputs">
97 <conditional name="input_type">
98 <param name="input_type_selector" value="single" />
99 <param name="read_type" value="-short" />
100 <param name="input" value="R1.fastq" ftype="fastq" />
101 </conditional>
102 </repeat>
103 <param name="strand_specific" value="" />
104 <output name="outfile" file="velveth_single.out">
105 <extra_files type="file" name='Sequences' value="velveth_single/Sequences" compare="diff" />
106 <extra_files type="file" name='Roadmaps' value="velveth_single/Roadmaps" compare="diff" />
107 </output>
108 </test>
109 <test>
110 <param name="hash_length" value="21" />
111 <repeat name="inputs">
112 <conditional name="input_type">
113 <param name="input_type_selector" value="single" />
114 <param name="read_type" value="-short" />
115 <param name="input" value="R1.fastq" ftype="fastq" />
116 </conditional>
117 </repeat>
118 <repeat name="inputs">
119 <param name="file_format" value="fastq" />
120 <conditional name="input_type">
121 <param name="input_type_selector" value="single" />
122 <param name="read_type" value="-short2" />
123 <param name="input" value="R2.fastq" ftype="fastq" />
124 </conditional>
125 </repeat>
126 <param name="strand_specific" value="" />
127 <output name="outfile" file="velveth_single.out">
128 <extra_files type="file" name='Sequences' value="velveth_single2/Sequences" compare="diff" />
129 <extra_files type="file" name='Roadmaps' value="velveth_single2/Roadmaps" compare="diff" />
153 </output> 130 </output>
154 </test> 131 </test>
155 </tests> 132 </tests>
156 <help><![CDATA[ 133 <help><![CDATA[
157 **What it does** 134 **What it does**