Mercurial > repos > iuc > rnaspades

annotate rnaspades.xml @ 1:dd4b53e5b34a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit a68a0ea372748c9d7ed2c96116b7b7c4c7585af4
author iuc
date Tue, 28 Mar 2017 10:53:06 -0400
parents a3e9e9b63502
children 5c7a049d755b
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dd4b53e5b34a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit a68a0ea372748c9d7ed2c96116b7b7c4c7585af4
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1 <tool id="rnaspades" name="rnaSPAdes" version="3.9.0.1">
0
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2 <description>assembler for RNA-Seq data</description>
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3 <requirements>
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4 <requirement type="package" version="3.9.0">spades</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command>
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10 <![CDATA[
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11 rnaspades.py -o .
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12 ## Forces unzipped output, faster
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13 --disable-gzip-output
1
dd4b53e5b34a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit a68a0ea372748c9d7ed2c96116b7b7c4c7585af4
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14 $draft $onlyassembler -t \${GALAXY_SLOTS:-4} $iontorrent -k $kmer
0
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15 ## Sequence files, libraries
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16 #for $i, $library in enumerate( $libraries, start=1 ):
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17 #if str( $library.lib_type ) == "paired_end":
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18 #set prefix = 'pe'
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19 #elif str( $library.lib_type ) == "mate_paired":
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20 #set prefix = 'mp'
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21 #elif str( $library.lib_type ) == "nxmate_paired":
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22 #set prefix = 'nxmate'
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23 #else:
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24 #set prefix = 'hqmp'
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25 #end if
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26 --$prefix$i-$library.orientation
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27 #for $file in $library.files
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28 #if $file.file_type.type == "separate":
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29 --$prefix$i-1 fastq:$file.file_type.fwd_reads
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30 --$prefix$i-2 fastq:$file.file_type.rev_reads
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31 #elif $file.file_type.type == "interleaved":
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32 --$prefix$i-12 fastq:$file.file_type.interleaved_reads
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33 #elif $file.file_type.type == "unpaired":
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34 --$prefix$i-s fastq:$file.file_type.unpaired_reads
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35 #elif $file.file_type.type == "paired-collection":
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36 --$prefix$i-1 fastq:$file.file_type.fastq_collection.forward
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37 --$prefix$i-2 fastq:$file.file_type.fastq_collection.reverse
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38 #end if
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39 #end for
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40 #end for
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41 #for $contig in $trusted_contigs:
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42 #if $contig:
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43 --trusted-contigs $contig.extension:$contig
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44 #end if
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45 #end for
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46 #for $contig in $untrusted_contigs:
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47 #if $contig:
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48 --untrusted-contigs $contig.extension:$contig
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49 #end if
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50 #end for
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51 ]]>
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52 </command>
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53 <inputs>
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54 <param argument="--draft-assembly" checked="False" falsevalue="" label="Draft assembly. Faster, but more error-prone" name="draft" truevalue="--draft-assembly" type="boolean" />
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55 <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" />
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56 <param argument="--iontorrent" checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" />
1
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57 <param argument="-k" max="127" label="k-mer size (must be odd and less than 128)" name="kmer" type="integer" value="55" />
0
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58 <repeat help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided." min="1" name="libraries" title="Libraries">
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59 <param label="Library type" name="lib_type" type="select">
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60 <option value="paired_end">Paired-end / Single reads</option>
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61 <option value="mate_paired">Mate pairs</option>
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62 <option value="high_mate_paired">High Quality Mate pairs</option>
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63 <option value="nxmate_paired">Lucigen NxMate pairs</option>
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64 </param>
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65 <param label="Orientation" name="orientation" type="select">
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66 <option selected="true" value="fr">-&gt; &lt;- (fr)</option>
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67 <option value="rf"><![CDATA[<- -> (rf)]]></option>
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68 <option value="ff"><![CDATA[-> -> (ff)]]></option>
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69 </param>
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70 <repeat min="1" name="files" title="Files">
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71 <conditional name="file_type">
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72 <param label="Select file format" name="type" type="select">
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73 <option value="separate">Separate input files</option>
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74 <option value="interleaved">Interleaved files</option>
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75 <option value="unpaired">Unpaired/Single reads</option>
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76 <option value="paired-collection">Paired List Collection</option>
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77 </param>
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78 <when value="separate">
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79 <param format="fastq" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" />
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80 <param format="fastq" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" />
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81 </when>
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82 <when value="interleaved">
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83 <param format="fastq" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" />
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84 </when>
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85 <when value="unpaired">
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86 <param format="fastq" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" />
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87 </when>
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88 <when value="paired-collection">
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89 <param collection_type="paired" format="fastq" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" />
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90 </when>
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91 </conditional>
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92 </repeat>
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93 </repeat>
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94 <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
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95 <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
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96 </inputs>
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97 <outputs>
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98 <data format="fasta" label="rnaSPAdes transcripts" name="output_transcripts" from_work_dir="transcripts.fasta" />
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99 </outputs>
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100 <tests>
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101 <test>
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102 <param name="lib_type" value="paired_end" />
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103 <param name="type" value="separate" />
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104 <param name="fwd_reads" value="rnaspades-in1-1.fq" ftype="fastq" />
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105 <param name="rev_reads" value="rnaspades-in1-2.fq" ftype="fastq" />
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106 <output name="output_transcripts" file="rnaspades-out1.fa" ftype="fasta" compare="re_match" lines_diff="1" />
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107 </test>
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108 </tests>
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109 <help>
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110 **What it does**
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111
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112 SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.
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113
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114 This wrapper runs SPAdes 3.9.0, collects the output, and throws away all the temporary files.
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115
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116 **License**
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117
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118 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
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119
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120 The original wrapper was written by Lionel Guy, Philip Mabon and was released under the GNU General Public License as published by the Free Software Foundation. The rnaSPAdes extension was developed by the Galaxy team.
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121
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122 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
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123
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124 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
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125
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126 ** Acknowledgments **
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127
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128 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
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129
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130 Nicola Soranzo fixed various bugs.
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131 </help>
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132 <citations>
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133 <citation type="doi">10.1089/cmb.2012.0021</citation>
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134 </citations>
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135 </tool>