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1 <tool id="masurca_simple" name="MaSuRCA simple" version="@TOOL_VERSION@+galaxy0">
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2 <description>The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit without config</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">4.0.6</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">masurca</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #set $long = 'false'
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11 #if $nanopore_input.np_input == "Yes":
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12 #if $pacbio_input.pb_input == "Yes":
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1
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13 cat '$nanopore_input.nano' '$pacbio_input.pacbio' > \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
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0
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14 #else:
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1
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15 ln -s '$nanopore_input.nano' \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
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0
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16 #end if
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17 #set $long = 'true'
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18 #elif $pacbio_input.pb_input == "Yes":
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1
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19 ln -s '$pacbio_input.pacbio' \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
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0
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20 #set $long = 'true'
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21 #end if
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22 masurca -t \${GALAXY_SLOTS:-8} -i
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23 #if str( $illumina_input.input_type ) == "single"
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24 '$illumina_input.fastq_input1'
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25 #elif str( $illumina_input.input_type ) == "paired"
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26 '$illumina_input.fastq_input1','$illumina_input.fastq_input2'
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27 #elif str( $illumina_input.input_type ) == "paired_collection"
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28 '$illumina_input.fastq_input1','$illumina_input.fastq_input2'
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29 #end if
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30 #if $long == "true":
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1
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31 -r \$_GALAXY_JOB_TMP_DIR/long.fastq.gz
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0
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32 #end if
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33 ]]></command>
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34 <inputs>
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35 <conditional name="illumina_input">
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36 <param name="input_type" type="select" label="Paired-end reads" help="Select between paired and paired collection">
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37 <option value="single">Single</option>
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38 <option value="paired">Paired</option>
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39 <option value="paired_collection">Paired Collection</option>
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40 </param>
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41 <when value="single">
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42 <param type="data" name="fastq_input1" format="fastqsanger,fastqsanger.gz"
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43 label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
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44 </when>
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45 <when value="paired">
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46 <param type="data" name="fastq_input1" format="fastqsanger,fastqsanger.gz"
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47 label="Select first set of reads" help="Specify dataset with forward reads"/>
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48 <param type="data" name="fastq_input2" format="fastqsanger,fastqsanger.gz"
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49 label="Select second set of reads" help="Specify dataset with reverse reads"/>
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50 </when>
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51 <when value="paired_collection">
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52 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
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53 </when>
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54 </conditional>
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55 <conditional name="nanopore_input">
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56 <param name="np_input" type="select" label="Use Nanopore long reads" help="Optional Nanopore reads must be in a single fasta or fastq file">
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57 <option value="No" selected="true">No</option>
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58 <option value="Yes">Yes</option>
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59 </param>
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60 <when value="No"/>
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61 <when value="Yes">
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62 <param type="data" name="nano" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="nanopore reads" />
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63 </when>
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64 </conditional>
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65 <conditional name="pacbio_input">
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66 <param name="pb_input" type="select" label="Use Pacbio long reads" help="Optional Pacbio reads must be in a single fasta or fastq file">
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67 <option value="No" selected="true">No</option>
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68 <option value="Yes">Yes</option>
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69 </param>
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70 <when value="No"/>
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71 <when value="Yes">
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72 <param type="data" name="pacbio" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="pacbio reads" />
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73 </when>
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74 </conditional>
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75 </inputs>
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76 <outputs>
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77 <data name="superReads" format="fasta" from_work_dir="work1/superReadSequences.fasta" label="${tool.name} on ${on_string}: superReads" />
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78 <data name="scaffold_prm" format="fasta" from_work_dir="CA.mr.*/primary.genome.scf.fasta" label="${tool.name} on ${on_string}: primary_genome" />
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79 <data name="scaffold_alt" format="fasta" from_work_dir="CA.mr.*/alternative.genome.scf.fasta" label="${tool.name} on ${on_string}: alternative_genome" />
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80 </outputs>
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81 <tests>
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82 <test>
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83 <conditional name="illumina_input">
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84 <param name="input_type" value="paired" />
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85 <param name="fastq_input1" value="phix_f.fq.gz"/>
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86 <param name="fastq_input2" value="phix_r.fq.gz"/>
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87 </conditional>
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88 <conditional name="nanopore_input">
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89 <param name="np_input" value="Yes" />
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90 <param name="nano" value="onp.fa"/>
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91 </conditional>
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92 <conditional name="pacbio_input">
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93 <param name="pb_input" value="No" />
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94 </conditional>
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1
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95 <output name="superReads" ftype="fasta">
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96 <assert_contents>
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97 <has_line_matching expression="^TCCGAAAGTGTTAACTT.*"/>
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98 </assert_contents>
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99 </output>
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0
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100 </test>
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101 </tests>
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102 <help><![CDATA[
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103
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104 This implementation of MaSuRCA is for small projects that only have PE
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105 Illumina reads (mandatory) and long reads from PACBIO or Oxford
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106 Nanopore or both. For larger projects and if you want to change the
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107 default options, you will need to run masurca_complex
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108
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109 ]]></help>
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110 <citations>
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111 <citation type="doi">10.1093/bioinformatics/btt476</citation>
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112 </citations>
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113 </tool>
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