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annotate quast.xml @ 0:736d51130b41 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
author iuc
date Tue, 13 Sep 2016 14:43:54 -0400
parents
children 0edbf19cf5eb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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1 <tool id="quast" name="Quast" version="4.1" >
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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2 <description>Genome assembly Quality</description>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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3 <requirements>
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iuc
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4 <requirement type="package" version="4.1">quast</requirement>
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5 </requirements>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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6 <stdio>
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7 <regex match="ERROR! exception caught!"
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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8 source="both"
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9 level="fatal"
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10 description="Something went wrong. Check the following errors : No labels..." />
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11 </stdio>
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12 <command>
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13 <![CDATA[
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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14 quast
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15 -o outputdir
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16 #if $gene_selection == "eukaryote":
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17 --eukaryote
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18 #else if $gene_selection == "metagenes":
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19 --meta
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20 #end if
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21 #if $input_ref:
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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22 -R '$input_ref'
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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23 #if $input_operon:
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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24 -O '$input_operon'
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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25 #end if
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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26 #if $annot:
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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27 -G '$annot'
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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28 #end if
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29 #end if
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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30 #if $input_size:
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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31 --est-ref-size $input_size
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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32 #end if
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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33 --min-contig $min_contig
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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34 --contig-thresholds $threshold_contig
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35 #for $k in $files:
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36 #if $k.type_file == "scaffold":
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37 -s
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38 #end if
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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39 $k.input
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40 #end for
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41 &&
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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42 mv outputdir/report.txt '$quast_out' &&
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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43 mv outputdir/report.tsv '$quast_tsv' &&
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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44 mv outputdir/report.tex '$quast_tex' &&
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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45 mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' &&
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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46 mv outputdir/report.html '$report_html'
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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47 ]]>
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48 </command>
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49 <inputs>
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50 <repeat name="files" title="Input assembly files" min="1">
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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51 <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file"/>
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52 <param name="type_file" type="select" label="Type of data">
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53 <option value="contig">Contig</option>
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54 <option value="scaffold">Scaffold</option>
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55 </param>
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56 </repeat>
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57 <param name="input_size" type="integer" label="Size of reference genome" optional="True" argument="--est-ref-size"
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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58 help="Estimated reference genome size (in bp) for computing NGx statistics, if known. This value will be used only if a reference genome file is not specified "/>
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59 <param name="input_ref" type="data" format="fasta" label="Reference File" optional="True" argument="-R"
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60 help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."/>
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61 <param name="annot" type="data" format="txt" label="Gene Annotations" optional="True" argument="-G"
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62 help="File with gene positions in the reference genome. "/>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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63 <param name="input_operon" type="data" format="txt" label="Operon Annotations" optional="True" argument="-O"
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64 help="File with operon positions in the reference genome"/>
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65 <param name="gene_selection" type="select" label="Type of organism">
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66 <option value="prokaryotes">Prokaryotes</option>
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67 <option value="eukaryote">Eukaryote</option>
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68 <option value="metagenes">Metagenomes</option>
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69 </param>
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70 <param name="min_contig" type="integer" value="500" label="Lower Threshold" argument="--min-contig"
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71 help="Set the lower threshold for a contig length. Shorter contigs won't be taken into account (default is 500)"/>
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72 <param name="threshold_contig" type="text" value="0,1000" label="Thresholds" argument="--contig-thresholds"
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73 help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.(default is 0,1000)"/>
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74 </inputs>
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75 <outputs>
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76 <data format="txt" name="quast_out" label="Quast report.txt" from_work_dir="Quast_report.txt"/>
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77 <data format="tsv" name="quast_tsv" label="Quast report.tsv" from_work_dir="Quast_report.tsv"/>
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78 <data format="tex" name="quast_tex" label="Quast report.tex" from_work_dir="Quast_report.tex"/>
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79 <data format="html" name="icarus" label="Icarus Contig size viewer" from_work_dir="Icarus.html"/>
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80 <data format="html" name="report_html" label="Quast report.html" from_work_dir="Quast_report.html"/>
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81 </outputs>
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82 <tests>
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83 <test>
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84 <param name="input" value="contigs_1.fasta"/>
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85 <param name="input.type_file" value="contig"/>
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86 <param name="gene_selection" value="prokaryotes"/>
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87 <output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/>
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88 </test>
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89 </tests>
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90 <help>
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91 <![CDATA[
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92 **Description**
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93
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94 Galaxy tool wrapper for the QUAST tool. Quast stands for QUality ASsessment Tool. It evaluates genome assemblies by computing various metrics.
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95
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96 -----
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97
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98 **Inputs and Outputs**
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99
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100 - Input:
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101 + The tool accepts assemblies and references in FASTA format.
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102 + The tool accepts annotation and operon files in:
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103 + GFF, versions 2 and 3 (note: feature/type field should be either "gene" or "operon")
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104 + the format used by NCBI for genes ("Summary (text)");
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105 + four tab-separated columns: sequence name, gene/operon id, start position, end position
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106
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107 - Output:
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108 + An assessment summary in plain text format
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109 + An assessment summary in tabulation separated values format
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110 + An assessment summary in LateX format
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111 + An assessment summary in HTML format
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112 + An HTML view of contig sizes wit Icarus
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113
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114
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115 ]]>
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116 </help>
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117
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118 <citations>
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119 <citation type="bibtex">@ARTICLE{a1,
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120 author = {Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler},
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121 title = {QUAST: quality assessment tool for genomce assemblies, Bioinformatics (2013) 29 (8): 1072-1075}
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122 }</citation>
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123 <citation type="bibtex">@misc{quast41,
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124 title = {{Quast} v4.1},
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125 howpublished = {http://bioinf.spbau.ru/quast},
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126 note = {Released May 2016}}
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127 }</citation>
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128 </citations>
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129 </tool>