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comparison velveth.xml @ 1:c397035f715d 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 16:57:48 +0000
parents c170448acc8a
children 088bf697a4ce
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0:c170448acc8a 1:c397035f715d
1 <tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.0"> 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 <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 export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" &&
14 #for $i in $inputs 13 mkdir -p '${outfile.extra_files_path}' &&
15 ${i.file_format} 14 velveth
16 ${i.read_type} 15 '$outfile.extra_files_path'
17 ${i.input} 16 $hash_length
18 #end for 17 #for $i in $inputs
19 </command> 18 -${i.input_type.input.ext}
19 ${i.input_type.read_type}
20 #if str( $i.input_type.input_type_selector ) == "paireds":
21 -separate '${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
29 ]]></command>
20 <inputs> 30 <inputs>
21 <param label="Hash Length" name="hash_length" type="select" 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."/>
22 <option value="11">11</option>
23 <option value="13">13</option>
24 <option value="15">15</option>
25 <option value="17">17</option>
26 <option value="19">19</option>
27 <option value="21" selected="yes">21</option>
28 <option value="23">23</option>
29 <option value="25">25</option>
30 <option value="27">27</option>
31 <option value="29">29</option>
32 </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."/> 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."/>
34 <repeat name="inputs" title="Input Files"> 33 <repeat name="inputs" title="Input Files">
35 <param label="file format" name="file_format" type="select"> 34 <conditional name="input_type">
36 <option value="-fasta" selected="yes">fasta</option> 35 <param name="input_type_selector" type="select" label="Choose the input type">
37 <option value="-fastq">fastq</option> 36 <option value="single" selected="true">Single ended</option>
38 <option value="-eland">eland</option> 37 <option value="paireds">separate paired end</option>
39 <option value="-gerald">gerald</option> 38 <option value="pairedi">interleaved paired end</option>
40 </param> 39 </param>
41 <param label="read type" name="read_type" type="select"> 40 <when value="single">
42 <option value="-short" selected="yes">short reads</option> 41 <param label="read type" name="read_type" type="select">
43 <option value="-shortPaired">shortPaired reads</option> 42 <option value="-short" selected="true">short reads</option>
44 <option value="-short2">short2 reads</option> 43 <option value="-short2">short2 reads</option>
45 <option value="-shortPaired2">shortPaired2 reads</option> 44 <option value="-short3">short3 reads</option>
46 <option value="-long">long reads</option> 45 <option value="-short4">short4 reads</option>
47 <option value="-longPaired">longPaired reads</option> 46 <option value="-long">long reads</option>
48 </param> 47 </param>
49 48 <param name="input" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Dataset"/>
50 <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>
51 </repeat> 72 </repeat>
52 </inputs> 73 </inputs>
53 <outputs> 74 <outputs>
54 <data format="velvet" name="out_file1" /> 75 <data format="velvet" name="outfile" />
55 </outputs> 76 </outputs>
56 <requirements>
57 <requirement type="package">velvet</requirement>
58 </requirements>
59 <tests> 77 <tests>
60 <test> 78 <test>
61 <param name="hash_length" value="21" /> 79 <param name="hash_length" value="21" />
62 <param name="read_type" value="-shortPaired" /> 80 <repeat name="inputs">
63 <!-- <repeat name="inputs"> --> 81 <conditional name="input_type">
64 <param name="file_format" value="fasta" /> 82 <param name="input_type_selector" value="paireds" />
65 <param name="read_type" value="shortPaired reads" /> 83 <param name="read_type" value="-shortPaired" />
66 <param name="input" value="velvet_test_reads.fa" ftype="fasta" /> 84 <param name="input1" value="R1.fastq" ftype="fastq" />
67 <!-- </repeat> --> 85 <param name="input2" value="R2.fastq" ftype="fastq" />
86 </conditional>
87 </repeat>
68 <param name="strand_specific" value="" /> 88 <param name="strand_specific" value="" />
69 <output name="out_file1" file="velveth_test1/output.html" lines_diff="4"> 89 <output name="outfile" file="velveth_paireds.out">
70 <extra_files type="file" name='Sequences' value="velveth_test1/Sequences" compare="diff" /> 90 <extra_files type="file" name='Sequences' value="velveth_paireds/Sequences" compare="diff" />
71 <extra_files type="file" name='Roadmaps' value="velveth_test1/Roadmaps" compare="diff" /> 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" />
72 </output> 130 </output>
73 </test> 131 </test>
74 </tests> 132 </tests>
75 <help> 133 <help><![CDATA[
76
77 **What it does** 134 **What it does**
78 135
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. 136 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.
80 137
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. 138 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 185 shortPaired
129 short2 (same as short, but for a separate insert-size library) 186 short2 (same as short, but for a separate insert-size library)
130 shortPaired2 (see above) 187 shortPaired2 (see above)
131 long (for Sanger, 454 or even reference sequences) 188 long (for Sanger, 454 or even reference sequences)
132 longPaired 189 longPaired
133 190 ]]></help>
134 </help>
135 <expand macro="citation"/> 191 <expand macro="citation"/>
136 </tool> 192 </tool>