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annotate rna_quast.xml @ 0:33c060ec0ac9 draft

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"planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
author iuc
date Mon, 19 Oct 2020 08:04:52 +0000
parents
children e989670c7fc7
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33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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1 <tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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2 <description>A Quality Assessment Tool for De Novo Transcriptome Assemblies</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.1.0</token>
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5 <xml name="element_matching_line" token_name="" token_expression="">
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6 <element name="@NAME@">
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7 <assert_contents><has_line_matching expression="@EXPRESSION@"/></assert_contents>
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8 </element>
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9 </xml>
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10 <xml name="element_has_text" token_name="" token_text="">
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11 <element name="@NAME@">
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12 <assert_contents><has_text text="@TEXT@"/></assert_contents>
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13 </element>
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14 </xml>
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15
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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16 <xml name="details_output_test" token_assembler="">
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17 <element name="@ASSEMBLER@">
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18 <element name="5000%-assembled.list"><assert_contents><has_n_lines n="0"/></assert_contents></element>
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19 <element name="9500%-assembled.list"><assert_contents><has_n_lines n="0"/></assert_contents></element>
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20 <expand macro="element_matching_line" name="alignment_metrics" expression="\s*== ALIGNMENT METRICS \(calculated with reference genome but without gene database\) ==\s*"/>
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21 <expand macro="element_matching_line" name="alignment_multiplicity" expression="unaligned=\d+ aligned=\d+ alignments=\d+\s*"/>
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22 <expand macro="element_matching_line" name="alignments_per_isoform" expression="avg=[\d.]+\s*"/>
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23 <expand macro="element_matching_line" name="basic_metrics" expression="\s*== BASIC TRANSCRIPTS METRICS \(calculated without reference genome and gene database\) ==\s*"/>
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24 <expand macro="element_matching_line" name="block_length" expression="avg=[\d.]+\s*"/>
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25 <expand macro="element_matching_line" name="blocks_per_alignment" expression="avg=[\d.]+\s+tot=\d+\s*"/>
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26 <expand macro="element_matching_line" name="database_metrics" expression="\s*== GENE DATABASE METRICS ==\s*"/>
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27 <expand macro="element_matching_line" name="misassemblies" expression="\s*== ALIGNMENT METRICS FOR MISASSEMBLED \(CHIMERIC\) TRANSCRIPTS \(calculated with reference genome or with gene database\) ==\s*"/>
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28 <expand macro="element_matching_line" name="mismatch_rate" expression="avg=[\d.]+\s+tot=\d+\s*"/>
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29 <expand macro="element_matching_line" name="sensitivity" expression="\s*== ASSEMBLY COMPLETENESS \(SENSITIVITY\) ==\s*"/>
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30 <expand macro="element_matching_line" name="specificity" expression="\s*== ASSEMBLY SPECIFICITY ==\s*"/>
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31 <expand macro="element_matching_line" name="transcript_length" expression="avg=[\d.]+\s*"/>
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32 <expand macro="element_matching_line" name="x-aligned" expression="avg=[\d.]+\s*"/>
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33 <expand macro="element_matching_line" name="x-assembled" expression="avg=[\d.]+\s*"/>
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34 <expand macro="element_matching_line" name="x-assembled_exons" expression="avg=[\d.]+\s*"/>
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35 <expand macro="element_matching_line" name="x-covered" expression="avg=[\d.]+\s*"/>
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36 <expand macro="element_matching_line" name="x-covered_exons" expression="avg=[\d.]+\s*"/>
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37 <expand macro="element_matching_line" name="x-matched" expression="avg=[\d.]+\s*"/>
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38 <expand macro="element_matching_line" name="x-matched_blocks" expression="avg=[\d.]+\s*"/>
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39 </element>
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40 </xml>
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41
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42 <xml name="txt_output_test" token_assembler="">
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43 <output name="short_report_txt">
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44 <assert_contents>
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45 <has_text text="SHORT SUMMARY REPORT"/>
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46 </assert_contents>
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47 </output>
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48 </xml>
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49 <xml name="tex_output_test" token_assembler="">
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50 <output name="short_report_tex">
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51 <assert_contents>
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52 <has_text text="Short summary report"/>
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53 <has_text text="end{document}"/>
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54 </assert_contents>
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55 </output>
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56 </xml>
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57 <xml name="tsv_output_test" token_assembler="">
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58 <output name="short_report_tsv">
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59 <assert_contents>
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60 <has_line_matching expression="^METRICS/TRANSCRIPTS\t.+$"/>
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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="pdf_output_test" token_assembler="">
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65 <output name="short_report_pdf">
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66 <assert_contents>
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67 <has_text text="rnaQUAST short report"/>
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68 </assert_contents>
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69 </output>
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70 </xml>
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71 </macros>
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72 <requirements>
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73 <requirement type="package" version="@TOOL_VERSION@">rnaquast</requirement>
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74 </requirements>
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75 <stdio>
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76 <regex match="Traceback " source="both" level="fatal" description="rnaQuast failed" />
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77 </stdio>
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78 <command detect_errors="exit_code"><![CDATA[
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79 #import re
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80 #for $i in $in_fasta
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81 ln -s '$i' '${re.sub('[^\w\-.]', '_', i.element_identifier)}' &&
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82 #end for
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83 #if $r
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84 #for $rf in $r
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85 ln -s '$rf' '${re.sub('[^\w\-.]', '_', rf.element_identifier)}' &&
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86 #end for
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87 #end if
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88 #if $gene_coordinates.use_gtf == "true"
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89 #for $g in $gene_coordinates.gtf
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90 ln -s '$g' '${re.sub('[^\w\-.]', '_', g.element_identifier)}' &&
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91 #end for
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92 #end if
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93 mkdir outputdir &&
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94 rnaQUAST.py
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95 --threads \${GALAXY_SLOTS:-1}
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96 --transcripts
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97 #for $i in $in_fasta
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98 '${re.sub('[^\w\-.]', '_', i.element_identifier)}'
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99 #end for
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100 $strand_specific
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101 #if $r
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102 -r
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103 #for $rf in $r
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104 '${re.sub('[^\w\-.]', '_', rf.element_identifier)}'
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105 #end for
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106 #end if
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107 #if $gene_coordinates.use_gtf == "true"
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108 --gtf
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109 #for $g in $gene_coordinates.gtf
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110 '${re.sub('[^\w\-.]', '_', g.element_identifier)}'
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111 #end for
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112 $gene_coordinates.disable_infer_genes
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113 $gene_coordinates.disable_infer_transcripts
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114 #end if
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115 $prokaryote
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116 --min_alignment '$min_alignment'
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117 #if "pdf" not in $out_sr and "plots" not in $out_add
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118 --no_plots
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119 #end if
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120 $blat
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121 $busco_lineage
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122 ##GeneMarkS-T is not available in conda $gene_mark
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123 $meta
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124 --lower_threshold $lower_threshold
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125 --upper_threshold $upper_threshold
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126 -o outputdir
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127
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128 && mkdir details
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129
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130 ## move per outputs that are generated for each input (outputdir/ASSEMBLER_output)
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131 ## to a joint dir (details) to make them discoverable
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132 ## also remove "ASSEMBLER." prefixes from files (otherwise the test macros don't work)
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133 #for $i in $in_fasta
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134 #set basename = os.path.splitext(re.sub('[^\w\-.]', '_', $i.element_identifier))[0]
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135 &&
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136 (for f in \$(find 'outputdir/'$basename'_output' -type f);
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137 do
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138 d=\$(dirname \$f | cut -d"/" -f2 | cut -d'_' -f1) &&
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139 mv \$f details/"\$d"_____"\$(basename \$f | sed 's/$basename\.//')";
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140 done)
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141 #end for
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142
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143 ## rename .list files to .txt files to make them detectable (format detection by extension)
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144 ## the final `true` seems needed since otherwise the `;` at the end is swallowed
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145 && find details/ -name "*.list" -exec mv {} {}.txt \;
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146 && true
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147 ]]></command>
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148 <inputs>
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149 <param name="in_fasta" type="data" format="fasta" multiple="true" label="Chromosomes/scaffolds file"/>
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150 <param name="strand_specific" argument="-ss" type="boolean" truevalue="-ss" falsevalue="" checked="false" label="Strand-specific"/>
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151 <param name="r" optional="true" argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
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152 <conditional name="gene_coordinates">
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153 <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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154 <option value="true" selected="true">Yes</option>
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155 <option value="false">No</option>
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156 </param>
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157 <when value="true">
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158 <param name="gtf" argument="--gtf" type="data" format="gtf,gff,gff3" multiple="true" label="GTF/GFF file"/>
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159 <param argument="--disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="false" label=" GTF file contains genes records?"/>
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160 <param argument="--disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="false" label="GTF file contains transcripts records?"/>
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161 </when>
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162 <when value="false">
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163 </when>
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164 </conditional>
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165 <param argument="--prokaryote" type="boolean" truevalue="--prokaryote" falsevalue="" checked="false" label="Is genome prokararyotic?"/>
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166 <param argument="--min_alignment" type="integer" value="50" label="Minimal alignment length to be used"/>
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167 <param argument="--blat" type="boolean" truevalue="--blat" falsevalue="" checked="false" label="Run with BLAT alignment tool instead of GMAP?" />
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168 <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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169 <!-- 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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170 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Meta Transcriptome" help="Run quality asessment for Meta Transcriptome"/>
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171 <param argument="--lower_threshold" type="integer" value="50" label="Lower threshold for x_assembled/covered/matched metrics."/>
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172 <param argument="--upper_threshold" type="integer" value="95" label="Upper threshold for x_assembled/covered/matched metrics."/>
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173 <param name="out_sr" type="select" multiple="true" label="Short report formats">
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174 <option value="tsv" selected="true">tabular</option>
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175 <option value="txt">txt</option>
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176 <option value="tex">tex</option>
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177 <option value="pdf" selected="true">pdf</option>
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178 </param>
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179 <param name="out_add" type="select" multiple="true" label="Additional outputs">
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180 <option value="logs">Logs</option>
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181 <option value="plots" selected="true">Plots (only for n>1)</option>
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182 <option value="comparison" selected="true">Comparison for Chromosomes/scaffolds files (only for n>1)</option>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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183 <option value="details" selected="true">Details per Chromosomes/scaffolds file</option>
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184 <option value="details_plots" selected="true">Details per Chromosomes/scaffolds file as plot</option>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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185 </param>
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186 </inputs>
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187
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188 <outputs>
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189 <data name="short_report_pdf" format="pdf" label="${tool.name} on ${on_string}: pdf report" from_work_dir="outputdir/short_report.pdf">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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190 <filter>"pdf" in out_sr</filter>
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191 </data>
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192 <data name="short_report_txt" format="txt" label="${tool.name} on ${on_string}: txt report" from_work_dir="outputdir/short_report.txt">
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193 <filter>"txt" in out_sr</filter>
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194 </data>
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195 <data name="short_report_tex" format="txt" label="${tool.name} on ${on_string}: tex report" from_work_dir="outputdir/short_report.tex">
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196 <filter>"tex" in out_sr</filter>
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197 </data>
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198 <data name="short_report_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv report" from_work_dir="outputdir/short_report.tsv">
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199 <filter>"tsv" in out_sr</filter>
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200 </data>
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201 <collection name="list_logs" type="list" label="${tool.name} on ${on_string}: logs" >
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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202 <discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.log" directory="outputdir/logs/" visible="false" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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203 <filter>"logs" in out_add</filter>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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204 </collection>
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205 <!-- note the output filter of the next two outputs checks if there is
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206 more than 1 input for in_fasta (for 1 its a HDA, for more list or HDAs) -->
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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207 <collection name="comparison_png" type="list" label="${tool.name} on ${on_string}: comparison plots" >
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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208 <discover_datasets ext="png" pattern="(?P&lt;name&gt;.+)\.png" directory="outputdir/comparison_output/" visible="false" recurse="true"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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209 <filter> isinstance(in_fasta, list) and "plots" in out_add</filter>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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210 </collection>
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211 <collection name="comparison" type="list" label="${tool.name} on ${on_string}: comparison" >
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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212 <discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.txt" directory="outputdir/comparison_output/" visible="false" recurse="true" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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213 <filter> isinstance(in_fasta, list) and "comparison" in out_add</filter>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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214 </collection>
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215 <collection name="details" type="list:list" label="${tool.name} on ${on_string}: detailed output">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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216 <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_____(?P&lt;identifier_1&gt;.+)\.(?P&lt;ext&gt;txt)" directory="details/" visible="false"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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217 <filter>"details" in out_add</filter>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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218 </collection>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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219 <collection name="details_png" type="list:list" label="${tool.name} on ${on_string}: detailed output plots">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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220 <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_____(?P&lt;identifier_1&gt;.+)\.(?P&lt;ext&gt;png)" directory="details/" visible="false"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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221 <filter>"details_plots" in out_add</filter>
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222 </collection>
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223 </outputs>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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224 <tests>
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225 <test expect_num_outputs="7">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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226 <param name="in_fasta" value="idba.fasta,Trinity.fasta" ftype="fasta" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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227 <param name="r" value="Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa" ftype="fasta" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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228 <conditional name="gene_coordinates">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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229 <param name="use_gtf" value="true" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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230 <param name="gtf" value="Saccharomyces_cerevisiae.R64-1-1.75.gtf" ftype="gtf" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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231 <param name="disable_infer_genes" value="true"/>
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232 <param name="disable_infer_transcripts" value="true"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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233 </conditional>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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234 <param name="out_sr" value="txt,tex,tsv" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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235 <param name="out_add" value="logs,comparison,plots,details" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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236 <expand macro="txt_output_test"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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237 <expand macro="tex_output_test"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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238 <expand macro="tsv_output_test"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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239 <output_collection name="comparison_png" type="list" count="15"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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240 <output_collection name="comparison" type="list" count="19"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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241 <output_collection name="list_logs" type="list" count="8"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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242 <output_collection name="details" type="list:list" count="2">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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243 <expand macro="details_output_test" assembler="Trinity"/>
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244 <expand macro="details_output_test" assembler="idba"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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245 </output_collection>
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246 </test>
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247 <test expect_num_outputs="6">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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248 <param name="in_fasta" value="Trinity.fasta" ftype="fasta" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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249 <conditional name="gene_coordinates">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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250 <param name="use_gtf" value="false" />
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251 </conditional>
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252 <param name="min_alignment" value="30" />
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253 <param name="lower_threshold" value="45" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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254 <param name="upper_threshold" value="95"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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255 <param name="out_sr" value="txt,tex,tsv,pdf" />
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256 <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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257
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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258 <expand macro="pdf_output_test"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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259 <expand macro="tex_output_test"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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260 <expand macro="tsv_output_test"/>
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261 <expand macro="txt_output_test"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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262 <output_collection name="list_logs" type="list">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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263 <expand macro="element_has_text" name="Trinity.GeneMarkS_T.err" text=""/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
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264 <expand macro="element_matching_line" name="rnaQUAST" expression="Thank you for using rnaQUAST!"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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265 </output_collection>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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266 <output_collection name="details_png" type="list:list" count="1">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
267 <element name="Trinity">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
268 <expand macro="element_has_text" name="Nx" text="PNG"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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269 <expand macro="element_has_text" name="transcript_length" text="PNG"/>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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270 </element>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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271 </output_collection>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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272 </test>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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273 </tests>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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274 <help><![CDATA[
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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275 **What is rnaQUAST**
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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276 - a quality assessment tool for de novo transcriptome assemblies
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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277 - 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
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diff changeset
278 - 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
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279
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
280 **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
281
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
282 - x-assembled (Exons)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
283 - Alignments per Isoform
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
284 - x-covered (Exons)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
285 - x-matched (Blocks)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
286 - gmap build logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
287
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
288 **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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diff changeset
289 - Reports
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
290 - Logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
291 - Alignement/Basic Metrics
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
292 - Misassemblies/ Specificity/ Sensitivity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
293 - Alignment multiplicity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
294 - Block/ Transcript Lentgh
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
295 - Blocks per alignment
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
296 - Mismatch rate
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
297 - x-aligned
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
298 - Nx
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
299 - Blocks per alignment
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
300 - gmap build logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
301
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
302 **Using rnaQuast without gene coordinates** you wont get:
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
303 - x-assembled (Exons)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
304 - Alignments per Isoform
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
305 - x-covered (Exons)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
306 - x-matched (Blocks)
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
307 - gmap build logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
308 - Database Metrics
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
309 - Alignment multiplicity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
310 - Mismatch rate
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
311 - NAx
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
312 - x-aligned
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
313 **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
314 - Reports
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
315 - Logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
316 - Alignement/Basic Metrics
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
317 - Misassemblies/Specificity/Sensitivity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
318 - Alignment multiplicity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
319 - Block/Transcript length
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
320 - Blocks per alignment
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
321 - Mismatch rate
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
322 - x-aligned
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
323 - Nx/NAx
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
324 - gmap build logs
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
325 - Database Metrics
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
326 - Alignment multiplicity
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
327 More informations, see citations.
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
328 ]]></help>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
329 <citations>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
330 <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
331 </citations>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
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diff changeset
332 </tool>