Mercurial > repos > iuc > rnaquast

annotate rna_quast.xml @ 4:f9f2ad782d8f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 790683fb2de6fd7e1275967b2aca93514cada7e9"
author iuc
date Thu, 20 Jan 2022 21:09:47 +0000
parents a9edbe21bf47
children f89e3c318453
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1 <tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
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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>
0
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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 <token name="@VERSION_SUFFIX@">1</token>
0
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9 <xml name="element_matching_line" token_name="" token_expression="">
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10 <element name="@NAME@">
1
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11 <assert_contents>
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12 <has_line_matching expression="@EXPRESSION@" />
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13 </assert_contents>
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14 </element>
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15 </xml>
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16 <xml name="element_has_text" token_name="" token_text="">
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17 <element name="@NAME@">
1
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18 <assert_contents>
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19 <has_text text="@TEXT@" />
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20 </assert_contents>
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21 </element>
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22 </xml>
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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>
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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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*" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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37 <expand macro="element_matching_line" name="alignments_per_isoform" expression="avg=[\d.]+\s*" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
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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*" />
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44 <expand macro="element_matching_line" name="sensitivity" expression="\s*== ASSEMBLY COMPLETENESS \(SENSITIVITY\) ==\s*" />
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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
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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>
1
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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.+$" />
0
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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" />
0
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83 </assert_contents>
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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>
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90 <stdio>
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91 <regex match="Traceback " source="both" level="fatal" description="rnaQuast failed" />
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92 </stdio>
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93 <command detect_errors="exit_code"><![CDATA[
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94 #import re
3
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95 #for $i in $transcripts
0
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96 ln -s '$i' '${re.sub('[^\w\-.]', '_', i.element_identifier)}' &&
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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
3
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112 #for $i in $transcripts
0
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113 '${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
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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
3
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136 #if $busco_option.busco == 'true'
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137 --busco $busco_option.lineage
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138 #end if
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139 ##$gene_mark
0
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140 $meta
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141 --lower_threshold $lower_threshold
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142 --upper_threshold $upper_threshold
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143 -o outputdir
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144
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145 && mkdir details
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146
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147 ## move per outputs that are generated for each input (outputdir/ASSEMBLER_output)
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148 ## to a joint dir (details) to make them discoverable
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149 ## also remove "ASSEMBLER." prefixes from files (otherwise the test macros don't work)
3
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150 #for $i in $transcripts
0
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151 #set basename = os.path.splitext(re.sub('[^\w\-.]', '_', $i.element_identifier))[0]
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152 &&
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153 (for f in \$(find 'outputdir/'$basename'_output' -type f);
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154 do
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155 d=\$(dirname \$f | cut -d"/" -f2 | cut -d'_' -f1) &&
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156 mv \$f details/"\$d"_____"\$(basename \$f | sed 's/$basename\.//')";
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157 done)
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158 #end for
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159
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160 ## rename .list files to .txt files to make them detectable (format detection by extension)
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161 ## the final `true` seems needed since otherwise the `;` at the end is swallowed
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162 && find details/ -name "*.list" -exec mv {} {}.txt \;
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163 && true
1
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164 ]]> </command>
0
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165 <inputs>
3
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166 <param argument="--transcripts" type="data" format="fasta" multiple="true" label="Transcripts" help="File(s) with transcripts in FASTA format."/>
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167 <param name="strand_specific" argument="-ss" type="boolean" truevalue="-ss" falsevalue="" checked="false" label="Strand-specific"
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168 help="Set if transcripts were assembled using strand-specific RNA-Seq data in order to benefit from knowing whether the transcript originated from the + or - strand"/>
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169 <param name="r" optional="true" argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" help="File with reference genome containing all chromosomes/scaffolds in FASTA forma." />
0
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170 <conditional name="gene_coordinates">
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171 <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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172 <option value="true" selected="true">Yes</option>
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173 <option value="false">No</option>
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174 </param>
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175 <when value="true">
1
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176 <param name="gtf" argument="--gtf" type="data" format="gtf,gff,gff3" multiple="true" label="GTF/GFF file" />
3
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177 <param argument="--disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="false" label=" GTF file contains genes records?"
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178 help="Use this option if your GTF file already contains genes records, otherwise gffutils will fix it. Note that gffutils may work for quite a long time"/>
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179 <param argument="--disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="false" label="GTF file contains transcripts records?" help="Is option if your GTF file already contains transcripts records, otherwise gffutils will fix it."/>
0
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180 </when>
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181 <when value="false">
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182 </when>
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183 </conditional>
3
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184 <param argument="--prokaryote" type="boolean" truevalue="--prokaryote" falsevalue="" checked="false" label="Is genome prokararyotic?" help="Use this option if the genome is prokaryotic."/>
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185 <param argument="--min_alignment" type="integer" value="50" label="Minimal alignment length to be used" help="Default value is 50"/>
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186 <param argument="--blat" type="boolean" truevalue="--blat" falsevalue="" checked="false" label="Run with BLAT alignment tool instead of GMAP?" help="Blat is especially useful for aligning long sequences and gapped mapping, which cannot be performed properly by other fast sequence mappers designed for short reads. " />
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187 <conditional name="busco_option">
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188 <param argument="--busco" type="select" label="Run BUSCO tool?" help="BUSCO allows to detect core genes in the assembled transcripts">
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189 <option value="false">Disabled</option>
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190 <option value="true">Enabled</option>
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191 </param>
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192 <when value="false"/>
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193 <when value="true">
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194 <param name="lineage" type="select" label="Lineage" help="Select a lineage for using BUSCO">
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195 <option value="metazoa">Metazoa</option>
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196 <option value="eukaryota">Eukaryota</option>
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197 <option value="arthropoda">Arthropoda</option>
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198 <option value="vertebrata">Vertebrata</option>
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199 <option value="fungi">Fungi</option>
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200 <option value="bacteria">Bacteria</option>
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201 </param>
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202 </when>
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203 </conditional>
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204 <!--param argument="-\-gene_mark" type="boolean" truevalue="-\-gene_mark" falsevalue="" checked="false" label="Run with GeneMarkS-T gene prediction tool?" help="GeneMarkS-T allows to predict genes in the assembled transcripts without reference genome"/-->
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205 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Meta Transcriptome" help="Run quality asessment for meta-transcriptome assemblies" />
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206 <param argument="--lower_threshold" type="integer" value="50" label="Lower threshold for x-assembled/covered/matched metrics." />
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207 <param argument="--upper_threshold" type="integer" value="95" label="Upper threshold for x-assembled/covered/matched metrics." />
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208 <param name="out_sr" type="select" multiple="true" label="Short report formats">
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209 <option value="tsv" selected="true">tabular</option>
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210 <option value="txt">txt</option>
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211 <option value="tex">tex</option>
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212 <option value="pdf" selected="true">pdf</option>
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213 </param>
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214 <param name="out_add" type="select" multiple="true" label="Additional outputs">
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215 <option value="logs">Logs</option>
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216 <option value="plots" selected="true">Plots (only for n>1)</option>
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217 <option value="comparison" selected="true">Comparison for Chromosomes/scaffolds files (only for n>1)</option>
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218 <option value="details" selected="true">Details per Chromosomes/scaffolds file</option>
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219 <option value="details_plots" selected="true">Details per Chromosomes/scaffolds file as plot</option>
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220 </param>
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221 </inputs>
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222
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223 <outputs>
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224 <data name="short_report_pdf" format="pdf" label="${tool.name} on ${on_string}: pdf report" from_work_dir="outputdir/short_report.pdf">
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225 <filter>"pdf" in out_sr</filter>
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226 </data>
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227 <data name="short_report_txt" format="txt" label="${tool.name} on ${on_string}: txt report" from_work_dir="outputdir/short_report.txt">
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228 <filter>"txt" in out_sr</filter>
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229 </data>
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230 <data name="short_report_tex" format="txt" label="${tool.name} on ${on_string}: tex report" from_work_dir="outputdir/short_report.tex">
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231 <filter>"tex" in out_sr</filter>
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232 </data>
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233 <data name="short_report_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv report" from_work_dir="outputdir/short_report.tsv">
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234 <filter>"tsv" in out_sr</filter>
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235 </data>
1
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236 <collection name="list_logs" type="list" label="${tool.name} on ${on_string}: logs">
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237 <discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.log" directory="outputdir/logs/" visible="false" />
0
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238 <filter>"logs" in out_add</filter>
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239 </collection>
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240 <!-- note the output filter of the next two outputs checks if there is
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241 more than 1 input for transcripts (for 1 its a HDA, for more list or HDAs) -->
1
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242 <collection name="comparison_png" type="list" label="${tool.name} on ${on_string}: comparison plots">
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243 <discover_datasets ext="png" pattern="(?P&lt;name&gt;.+)\.png" directory="outputdir/comparison_output/" visible="false" recurse="true" />
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244 <filter> isinstance(transcripts, list) and "plots" in out_add</filter>
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245 </collection>
1
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246 <collection name="comparison" type="list" label="${tool.name} on ${on_string}: comparison">
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247 <discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.txt" directory="outputdir/comparison_output/" visible="false" recurse="true" />
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248 <filter> isinstance(transcripts, list) and "comparison" in out_add</filter>
0
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249 </collection>
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250 <collection name="details" type="list:list" label="${tool.name} on ${on_string}: detailed output">
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251 <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_____(?P&lt;identifier_1&gt;.+)\.(?P&lt;ext&gt;txt)" directory="details/" visible="false" />
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252 <filter>"details" in out_add</filter>
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253 </collection>
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254 <collection name="details_png" type="list:list" label="${tool.name} on ${on_string}: detailed output plots">
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255 <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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256 <filter>"details_plots" in out_add</filter>
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257 </collection>
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258 </outputs>
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259 <tests>
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260 <test expect_num_outputs="7">
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261 <param name="transcripts" value="idba.fasta,Trinity.fasta" ftype="fasta" />
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262 <param name="r" value="Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa" ftype="fasta" />
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263 <conditional name="gene_coordinates">
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264 <param name="use_gtf" value="true" />
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265 <param name="gtf" value="Saccharomyces_cerevisiae.R64-1-1.75.gtf" ftype="gtf" />
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266 <param name="disable_infer_genes" value="true" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
267 <param name="disable_infer_transcripts" value="true" />
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
268 </conditional>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
269 <param name="out_sr" value="txt,tex,tsv" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
270 <param name="out_add" value="logs,comparison,plots,details" />
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
271 <expand macro="txt_output_test" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
272 <expand macro="tex_output_test" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
273 <expand macro="tsv_output_test" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
274 <output_collection name="comparison_png" type="list" count="15" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
275 <output_collection name="comparison" type="list" count="19" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
276 <output_collection name="list_logs" type="list" count="8" />
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
277 <output_collection name="details" type="list:list" count="2">
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
278 <expand macro="details_output_test" assembler="Trinity" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
279 <expand macro="details_output_test" assembler="idba" />
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
280 </output_collection>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
281 </test>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
282 <test expect_num_outputs="6">
3
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
283 <param name="transcripts" value="Trinity.fasta" ftype="fasta" />
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
284 <conditional name="gene_coordinates">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
285 <param name="use_gtf" value="false" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
286 </conditional>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
287 <param name="min_alignment" value="30" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
288 <param name="lower_threshold" value="45" />
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
289 <param name="upper_threshold" value="95" />
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
290 <param name="out_sr" value="txt,tex,tsv,pdf" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
291 <param name="out_add" value="logs,details_plots" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
292
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
293 <expand macro="pdf_output_test" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
294 <expand macro="tex_output_test" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
295 <expand macro="tsv_output_test" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
296 <expand macro="txt_output_test" />
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
297 <output_collection name="list_logs" type="list">
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
298 <expand macro="element_has_text" name="Trinity.GeneMarkS_T.err" text="" />
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
299 <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"
iuc
parents:
diff changeset
300 </output_collection>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
301 <output_collection name="details_png" type="list:list" count="1">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
302 <element name="Trinity">
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
303 <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
304 <expand macro="element_has_text" name="transcript_length" text="PNG" />
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
305 </element>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
306 </output_collection>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
307 </test>
3
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
308 <test expect_num_outputs="6">
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
309 <param name="transcripts" value="Trinity.fasta" ftype="fasta" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
310 <conditional name="gene_coordinates">
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
311 <param name="use_gtf" value="false" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
312 </conditional>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
313 <param name="min_alignment" value="30" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
314 <param name="lower_threshold" value="45" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
315 <param name="upper_threshold" value="95" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
316 <param name="out_sr" value="txt,tex,tsv,pdf" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
317 <param name="out_add" value="logs,details_plots" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
318 <conditional name="busco_option">
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
319 <param name="busco" value="true"/>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
320 <param name="lineage" value="metazoa"/>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
321 </conditional>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
322 <expand macro="pdf_output_test" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
323 <expand macro="tex_output_test" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
324 <expand macro="tsv_output_test" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
325 <expand macro="txt_output_test" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
326 <output_collection name="list_logs" type="list">
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
327 <expand macro="element_has_text" name="Trinity.GeneMarkS_T.err" text="" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
328 <expand macro="element_matching_line" name="rnaQUAST" expression="Thank you for using rnaQUAST!" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
329 </output_collection>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
330 <output_collection name="details_png" type="list:list" count="1">
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
331 <element name="Trinity">
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
332 <expand macro="element_has_text" name="Nx" text="PNG" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
333 <expand macro="element_has_text" name="transcript_length" text="PNG" />
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
334 </element>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
335 </output_collection>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
336 <assert_command>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
337 <has_text text="--busco metazoa"/>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
338 </assert_command>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
339 </test>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
340 </tests>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
341 <help><![CDATA[
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
342 **What is rnaQUAST**
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
343 - a quality assessment tool for de novo transcriptome assemblies
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
344 - 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"
iuc
parents:
diff changeset
345 - 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"
iuc
parents:
diff changeset
346
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
347 **Using rnaQuast without reference** you wont get:
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
348
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
349 - x-assembled (Exons)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
350 - Alignments per Isoform
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
351 - x-covered (Exons)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
352 - x-matched (Blocks)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
353 - gmap build logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
354
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
355 **Using rnaQuast with reference** you will get:
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
356 - Reports
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
357 - Logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
358 - Alignement/Basic Metrics
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
359 - Misassemblies/ Specificity/ Sensitivity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
360 - Alignment multiplicity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
361 - Block/ Transcript Lentgh
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
362 - Blocks per alignment
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
363 - Mismatch rate
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
364 - x-aligned
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
365 - Nx
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
366 - Blocks per alignment
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
367 - gmap build logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
368
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
369 **Using rnaQuast without gene coordinates** you wont get:
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
370 - x-assembled (Exons)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
371 - Alignments per Isoform
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
372 - x-covered (Exons)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
373 - x-matched (Blocks)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
374 - gmap build logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
375 - Database Metrics
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
376 - Alignment multiplicity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
377 - Mismatch rate
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
378 - NAx
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
379 - x-aligned
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
380 **Using rnaQuast with gene coordinates** you will get:
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
381 - Reports
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
382 - Logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
383 - Alignement/Basic Metrics
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
384 - Misassemblies/Specificity/Sensitivity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
385 - Alignment multiplicity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
386 - Block/Transcript length
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
387 - Blocks per alignment
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
388 - Mismatch rate
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
389 - x-aligned
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
390 - Nx/NAx
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
391 - gmap build logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
392 - Database Metrics
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
393 - Alignment multiplicity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
394 More informations, see citations.
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
395 ]]> </help>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
396 <citations>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
397 <citation type="doi">10.1093/bioinformatics/btw218 </citation>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
398 </citations>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
399 </tool>