Mercurial > repos > iuc > rnaquast

annotate rna_quast.xml @ 2:96f74538896e draft

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"planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit a88588e97947741fdf17e95fbeb851a296c4eb1c"
author iuc
date Tue, 19 Oct 2021 11:02:19 +0000
parents e989670c7fc7
children a9edbe21bf47
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1 <tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@">
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2 <description>A Quality Assessment Tool for De Novo Transcriptome Assemblies</description>
2
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3 <xrefs>
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4 <xref type="bio.tools">rnaQUAST</xref>
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5 </xrefs>
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6 <macros>
2
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7 <token name="@TOOL_VERSION@">2.2.1</token>
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8 <xml name="element_matching_line" token_name="" token_expression="">
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9 <element name="@NAME@">
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10 <assert_contents>
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11 <has_line_matching expression="@EXPRESSION@" />
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12 </assert_contents>
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13 </element>
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14 </xml>
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15 <xml name="element_has_text" token_name="" token_text="">
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16 <element name="@NAME@">
1
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17 <assert_contents>
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18 <has_text text="@TEXT@" />
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19 </assert_contents>
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20 </element>
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21 </xml>
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22
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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23 <xml name="details_output_test" token_assembler="">
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24 <element name="@ASSEMBLER@">
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25 <element name="5000%-assembled.list">
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26 <assert_contents>
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27 <has_n_lines n="0" />
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28 </assert_contents>
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29 </element>
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30 <element name="9500%-assembled.list">
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31 <assert_contents>
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32 <has_n_lines n="0" />
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33 </assert_contents>
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34 </element>
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35 <expand macro="element_matching_line" name="alignment_metrics" expression="\s*== ALIGNMENT METRICS \(calculated with reference genome but without gene database\) ==\s*" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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36 <expand macro="element_matching_line" name="alignment_multiplicity" expression="unaligned=\d+ aligned=\d+ alignments=\d+\s*" />
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37 <expand macro="element_matching_line" name="alignments_per_isoform" expression="avg=[\d.]+\s*" />
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38 <expand macro="element_matching_line" name="basic_metrics" expression="\s*== BASIC TRANSCRIPTS METRICS \(calculated without reference genome and gene database\) ==\s*" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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39 <expand macro="element_matching_line" name="block_length" expression="avg=[\d.]+\s*" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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40 <expand macro="element_matching_line" name="blocks_per_alignment" expression="avg=[\d.]+\s+tot=\d+\s*" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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41 <expand macro="element_matching_line" name="database_metrics" expression="\s*== GENE DATABASE METRICS ==\s*" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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42 <expand macro="element_matching_line" name="misassemblies" expression="\s*== ALIGNMENT METRICS FOR MISASSEMBLED \(CHIMERIC\) TRANSCRIPTS \(calculated with reference genome or with gene database\) ==\s*" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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43 <expand macro="element_matching_line" name="mismatch_rate" expression="avg=[\d.]+\s+tot=\d+\s*" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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44 <expand macro="element_matching_line" name="sensitivity" expression="\s*== ASSEMBLY COMPLETENESS \(SENSITIVITY\) ==\s*" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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45 <expand macro="element_matching_line" name="specificity" expression="\s*== ASSEMBLY SPECIFICITY ==\s*" />
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46 <expand macro="element_matching_line" name="transcript_length" expression="avg=[\d.]+\s*" />
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47 <expand macro="element_matching_line" name="x-aligned" expression="avg=[\d.]+\s*" />
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48 <expand macro="element_matching_line" name="x-assembled" expression="avg=[\d.]+\s*" />
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49 <expand macro="element_matching_line" name="x-assembled_exons" expression="avg=[\d.]+\s*" />
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50 <expand macro="element_matching_line" name="x-covered" expression="avg=[\d.]+\s*" />
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51 <expand macro="element_matching_line" name="x-covered_exons" expression="avg=[\d.]+\s*" />
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52 <expand macro="element_matching_line" name="x-matched" expression="avg=[\d.]+\s*" />
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53 <expand macro="element_matching_line" name="x-matched_blocks" expression="avg=[\d.]+\s*" />
0
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54 </element>
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55 </xml>
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56
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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57 <xml name="txt_output_test" token_assembler="">
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58 <output name="short_report_txt">
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59 <assert_contents>
1
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60 <has_text text="SHORT SUMMARY REPORT" />
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61 </assert_contents>
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62 </output>
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63 </xml>
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64 <xml name="tex_output_test" token_assembler="">
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65 <output name="short_report_tex">
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66 <assert_contents>
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67 <has_text text="Short summary report" />
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68 <has_text text="end{document}" />
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69 </assert_contents>
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70 </output>
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71 </xml>
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72 <xml name="tsv_output_test" token_assembler="">
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73 <output name="short_report_tsv">
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74 <assert_contents>
1
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75 <has_line_matching expression="^METRICS/TRANSCRIPTS\t.+$" />
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76 </assert_contents>
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77 </output>
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78 </xml>
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79 <xml name="pdf_output_test" token_assembler="">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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80 <output name="short_report_pdf">
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81 <assert_contents>
1
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82 <has_text text="rnaQUAST short report" />
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83 </assert_contents>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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84 </output>
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85 </xml>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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86 </macros>
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87 <requirements>
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88 <requirement type="package" version="@TOOL_VERSION@">rnaquast</requirement>
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89 </requirements>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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90 <stdio>
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91 <regex match="Traceback " source="both" level="fatal" description="rnaQuast failed" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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92 </stdio>
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93 <command detect_errors="exit_code"><![CDATA[
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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94 #import re
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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95 #for $i in $in_fasta
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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96 ln -s '$i' '${re.sub('[^\w\-.]', '_', i.element_identifier)}' &&
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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97 #end for
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98 #if $r
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99 #for $rf in $r
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100 ln -s '$rf' '${re.sub('[^\w\-.]', '_', rf.element_identifier)}' &&
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101 #end for
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102 #end if
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103 #if $gene_coordinates.use_gtf == "true"
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104 #for $g in $gene_coordinates.gtf
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105 ln -s '$g' '${re.sub('[^\w\-.]', '_', g.element_identifier)}' &&
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106 #end for
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107 #end if
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108 mkdir outputdir &&
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109 rnaQUAST.py
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110 --threads \${GALAXY_SLOTS:-1}
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111 --transcripts
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112 #for $i in $in_fasta
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113 '${re.sub('[^\w\-.]', '_', i.element_identifier)}'
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114 #end for
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115 $strand_specific
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116 #if $r
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117 -r
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118 #for $rf in $r
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119 '${re.sub('[^\w\-.]', '_', rf.element_identifier)}'
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120 #end for
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121 #end if
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122 #if $gene_coordinates.use_gtf == "true"
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123 --gtf
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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124 #for $g in $gene_coordinates.gtf
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125 '${re.sub('[^\w\-.]', '_', g.element_identifier)}'
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126 #end for
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127 $gene_coordinates.disable_infer_genes
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128 $gene_coordinates.disable_infer_transcripts
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129 #end if
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130 $prokaryote
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131 --min_alignment '$min_alignment'
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132 #if "pdf" not in $out_sr and "plots" not in $out_add
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133 --no_plots
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134 #end if
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135 $blat
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136 $busco_lineage
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137 ##GeneMarkS-T is not available in conda $gene_mark
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138 $meta
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139 --lower_threshold $lower_threshold
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140 --upper_threshold $upper_threshold
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141 -o outputdir
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142
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143 && mkdir details
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144
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145 ## move per outputs that are generated for each input (outputdir/ASSEMBLER_output)
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146 ## to a joint dir (details) to make them discoverable
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147 ## also remove "ASSEMBLER." prefixes from files (otherwise the test macros don't work)
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148 #for $i in $in_fasta
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149 #set basename = os.path.splitext(re.sub('[^\w\-.]', '_', $i.element_identifier))[0]
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150 &&
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151 (for f in \$(find 'outputdir/'$basename'_output' -type f);
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152 do
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153 d=\$(dirname \$f | cut -d"/" -f2 | cut -d'_' -f1) &&
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154 mv \$f details/"\$d"_____"\$(basename \$f | sed 's/$basename\.//')";
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155 done)
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156 #end for
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157
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158 ## rename .list files to .txt files to make them detectable (format detection by extension)
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159 ## the final `true` seems needed since otherwise the `;` at the end is swallowed
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160 && find details/ -name "*.list" -exec mv {} {}.txt \;
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161 && true
1
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162 ]]> </command>
0
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163 <inputs>
1
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164 <param name="in_fasta" type="data" format="fasta" multiple="true" label="Chromosomes/scaffolds file" />
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165 <param name="strand_specific" argument="-ss" type="boolean" truevalue="-ss" falsevalue="" checked="false" label="Strand-specific" />
0
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166 <param name="r" optional="true" argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
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167 <conditional name="gene_coordinates">
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168 <param name="use_gtf" type="select" label="Use file with gene coordinates in GTF/GFF format?" help="We recommend to use files downloaded from GENCODE or Ensembl.">
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169 <option value="true" selected="true">Yes</option>
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170 <option value="false">No</option>
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171 </param>
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172 <when value="true">
1
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173 <param name="gtf" argument="--gtf" type="data" format="gtf,gff,gff3" multiple="true" label="GTF/GFF file" />
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174 <param argument="--disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="false" label=" GTF file contains genes records?" />
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175 <param argument="--disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="false" label="GTF file contains transcripts records?" />
0
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176 </when>
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177 <when value="false">
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178 </when>
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179 </conditional>
1
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180 <param argument="--prokaryote" type="boolean" truevalue="--prokaryote" falsevalue="" checked="false" label="Is genome prokararyotic?" />
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181 <param argument="--min_alignment" type="integer" value="50" label="Minimal alignment length to be used" />
0
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182 <param argument="--blat" type="boolean" truevalue="--blat" falsevalue="" checked="false" label="Run with BLAT alignment tool instead of GMAP?" />
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183 <param argument="--busco_lineage" type="boolean" truevalue="--busco_lineage" falsevalue="" checked="false" label="Run BUSCO tool?" help="The BUSCO tool detects core genes in the assembly. Use this option to provide path to the BUSCO lineage data (Eukaryota, Metazoa, Arthropoda, Vertebrata or Fungi)." />
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184 <!-- GeneMarkS-T is not available in conda <param argument="\-\-gene_mark" type="boolean" truevalue="\-\-gene_mark" falsevalue="" checked="false" label="Run with GeneMarkS-T gene prediction tool?"/>-->
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185 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Meta Transcriptome" help="Run quality asessment for Meta Transcriptome" />
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186 <param argument="--lower_threshold" type="integer" value="50" label="Lower threshold for x_assembled/covered/matched metrics." />
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187 <param argument="--upper_threshold" type="integer" value="95" label="Upper threshold for x_assembled/covered/matched metrics." />
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188 <param name="out_sr" type="select" multiple="true" label="Short report formats">
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189 <option value="tsv" selected="true">tabular</option>
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190 <option value="txt">txt</option>
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191 <option value="tex">tex</option>
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192 <option value="pdf" selected="true">pdf</option>
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193 </param>
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194 <param name="out_add" type="select" multiple="true" label="Additional outputs">
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195 <option value="logs">Logs</option>
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196 <option value="plots" selected="true">Plots (only for n>1)</option>
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197 <option value="comparison" selected="true">Comparison for Chromosomes/scaffolds files (only for n>1)</option>
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198 <option value="details" selected="true">Details per Chromosomes/scaffolds file</option>
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199 <option value="details_plots" selected="true">Details per Chromosomes/scaffolds file as plot</option>
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200 </param>
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201 </inputs>
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202
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203 <outputs>
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204 <data name="short_report_pdf" format="pdf" label="${tool.name} on ${on_string}: pdf report" from_work_dir="outputdir/short_report.pdf">
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205 <filter>"pdf" in out_sr</filter>
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206 </data>
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207 <data name="short_report_txt" format="txt" label="${tool.name} on ${on_string}: txt report" from_work_dir="outputdir/short_report.txt">
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208 <filter>"txt" in out_sr</filter>
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209 </data>
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210 <data name="short_report_tex" format="txt" label="${tool.name} on ${on_string}: tex report" from_work_dir="outputdir/short_report.tex">
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211 <filter>"tex" in out_sr</filter>
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212 </data>
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213 <data name="short_report_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv report" from_work_dir="outputdir/short_report.tsv">
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214 <filter>"tsv" in out_sr</filter>
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215 </data>
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216 <collection name="list_logs" type="list" label="${tool.name} on ${on_string}: logs">
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217 <discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.log" directory="outputdir/logs/" visible="false" />
0
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218 <filter>"logs" in out_add</filter>
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219 </collection>
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220 <!-- note the output filter of the next two outputs checks if there is
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221 more than 1 input for in_fasta (for 1 its a HDA, for more list or HDAs) -->
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222 <collection name="comparison_png" type="list" label="${tool.name} on ${on_string}: comparison plots">
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223 <discover_datasets ext="png" pattern="(?P&lt;name&gt;.+)\.png" directory="outputdir/comparison_output/" visible="false" recurse="true" />
0
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224 <filter> isinstance(in_fasta, list) and "plots" in out_add</filter>
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225 </collection>
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226 <collection name="comparison" type="list" label="${tool.name} on ${on_string}: comparison">
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227 <discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.txt" directory="outputdir/comparison_output/" visible="false" recurse="true" />
0
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228 <filter> isinstance(in_fasta, list) and "comparison" in out_add</filter>
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229 </collection>
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230 <collection name="details" type="list:list" label="${tool.name} on ${on_string}: detailed output">
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231 <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_____(?P&lt;identifier_1&gt;.+)\.(?P&lt;ext&gt;txt)" directory="details/" visible="false" />
0
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232 <filter>"details" in out_add</filter>
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233 </collection>
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234 <collection name="details_png" type="list:list" label="${tool.name} on ${on_string}: detailed output plots">
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235 <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_____(?P&lt;identifier_1&gt;.+)\.(?P&lt;ext&gt;png)" directory="details/" visible="false" />
0
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236 <filter>"details_plots" in out_add</filter>
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237 </collection>
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238 </outputs>
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239 <tests>
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240 <test expect_num_outputs="7">
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241 <param name="in_fasta" value="idba.fasta,Trinity.fasta" ftype="fasta" />
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242 <param name="r" value="Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa" ftype="fasta" />
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243 <conditional name="gene_coordinates">
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244 <param name="use_gtf" value="true" />
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245 <param name="gtf" value="Saccharomyces_cerevisiae.R64-1-1.75.gtf" ftype="gtf" />
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246 <param name="disable_infer_genes" value="true" />
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247 <param name="disable_infer_transcripts" value="true" />
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248 </conditional>
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249 <param name="out_sr" value="txt,tex,tsv" />
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250 <param name="out_add" value="logs,comparison,plots,details" />
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251 <expand macro="txt_output_test" />
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252 <expand macro="tex_output_test" />
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253 <expand macro="tsv_output_test" />
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254 <output_collection name="comparison_png" type="list" count="15" />
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255 <output_collection name="comparison" type="list" count="19" />
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256 <output_collection name="list_logs" type="list" count="8" />
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257 <output_collection name="details" type="list:list" count="2">
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258 <expand macro="details_output_test" assembler="Trinity" />
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259 <expand macro="details_output_test" assembler="idba" />
0
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260 </output_collection>
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261 </test>
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262 <test expect_num_outputs="6">
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263 <param name="in_fasta" value="Trinity.fasta" ftype="fasta" />
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264 <conditional name="gene_coordinates">
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265 <param name="use_gtf" value="false" />
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266 </conditional>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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267 <param name="min_alignment" value="30" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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268 <param name="lower_threshold" value="45" />
1
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269 <param name="upper_threshold" value="95" />
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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270 <param name="out_sr" value="txt,tex,tsv,pdf" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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271 <param name="out_add" value="logs,details_plots" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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272
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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diff changeset
273 <expand macro="pdf_output_test" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
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diff changeset
274 <expand macro="tex_output_test" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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diff changeset
275 <expand macro="tsv_output_test" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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276 <expand macro="txt_output_test" />
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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277 <output_collection name="list_logs" type="list">
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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278 <expand macro="element_has_text" name="Trinity.GeneMarkS_T.err" text="" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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279 <expand macro="element_matching_line" name="rnaQUAST" expression="Thank you for using rnaQUAST!" />
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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280 </output_collection>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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281 <output_collection name="details_png" type="list:list" count="1">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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diff changeset
282 <element name="Trinity">
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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parents: 0
diff changeset
283 <expand macro="element_has_text" name="Nx" text="PNG" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
284 <expand macro="element_has_text" name="transcript_length" text="PNG" />
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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285 </element>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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286 </output_collection>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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287 </test>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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288 </tests>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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289 <help><![CDATA[
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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290 **What is rnaQUAST**
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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291 - a quality assessment tool for de novo transcriptome assemblies
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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292 - evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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293 - calculates various metrics that demonstrate completeness and correctness levels of the assembled transcripts
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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294
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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295 **Using rnaQuast without reference** you wont get:
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
296
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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297 - x-assembled (Exons)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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298 - Alignments per Isoform
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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299 - x-covered (Exons)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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300 - x-matched (Blocks)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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301 - gmap build logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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302
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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303 **Using rnaQuast with reference** you will get:
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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304 - Reports
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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305 - Logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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306 - Alignement/Basic Metrics
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
307 - Misassemblies/ Specificity/ Sensitivity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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308 - Alignment multiplicity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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309 - Block/ Transcript Lentgh
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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310 - Blocks per alignment
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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311 - Mismatch rate
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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312 - x-aligned
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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313 - Nx
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
314 - Blocks per alignment
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
315 - gmap build logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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316
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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317 **Using rnaQuast without gene coordinates** you wont get:
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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318 - x-assembled (Exons)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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319 - Alignments per Isoform
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
320 - x-covered (Exons)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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321 - x-matched (Blocks)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
322 - gmap build logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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323 - Database Metrics
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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324 - Alignment multiplicity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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325 - Mismatch rate
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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326 - NAx
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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327 - x-aligned
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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328 **Using rnaQuast with gene coordinates** you will get:
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
329 - Reports
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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330 - Logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
331 - Alignement/Basic Metrics
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
332 - Misassemblies/Specificity/Sensitivity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
333 - Alignment multiplicity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
334 - Block/Transcript length
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
335 - Blocks per alignment
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
336 - Mismatch rate
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
337 - x-aligned
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
338 - Nx/NAx
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
339 - gmap build logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
340 - Database Metrics
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
341 - Alignment multiplicity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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342 More informations, see citations.
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
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343 ]]> </help>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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344 <citations>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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345 <citation type="doi">10.1093/bioinformatics/btw218 </citation>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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346 </citations>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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347 </tool>