annotate gffcompare.xml @ 16:24d0a81802d6 draft

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author enios
date Sat, 22 May 2021 07:30:49 +0000
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1 <tool id="gffcompare" name="GffCompare">
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2 <description>compare assembled transcripts to a reference annotation</description>
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3 <requirements>
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4 <container type="docker">bianca7/lncrna:gffcompare</container>
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5 </requirements>
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6 <!--version_command>gffcompare -v | awk '{print $2}'</version_command-->
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7 <command detect_errors="aggressive"><![CDATA[
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8 #import re
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9
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10 #set escaped_element_identifiers = [re.sub('[^\w\-]', '_', str(_.element_identifier)) for _ in $gffinputs]
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11 #for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers):
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12 ln -s '$input' '$escaped_element_identifier' &&
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13 #end for
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14 #if $seq_data.use_seq_data == "Yes":
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15 #if $seq_data.seq_source.index_source == "history":
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16 ln -s '$seq_data.seq_source.ref_file' ref_seq.fa &&
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17 #else:
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18 ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa &&
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19 #end if
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20 #end if
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21
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22 #if $annotation.use_ref_annotation == "Yes":
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23 #if $annotation.ref_source.ref_source_sel == "history":
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24 ln -s '$annotation.ref_source.reference_annotation' ref_annotation &&
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25 #else
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26 ln -s '$annotation.ref_source.index.fields.path' ref_annotation &&
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27 #end if
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28 #end if
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29
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30 gffcompare
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31 ## Use annotation reference?
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32 #if $annotation.use_ref_annotation == "Yes":
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33 -r ref_annotation
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34 $annotation.ignore_nonoverlapping_reference
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35 $annotation.ignore_nonoverlapping_transfrags
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36 $annotation.strict_match
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37 #end if
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38 #if $annotation.refmap_tmap == "":
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39 -T
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40 #end if
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41
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42 ## Use sequence data?
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43 #if $seq_data.use_seq_data == "Yes":
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44 -s ref_seq.fa
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45 #end if
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46
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47 $discard_single_exon
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48 $discard_duplicates
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49 $no_merge
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50 -e $max_dist_exon
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51 -d $max_dist_group
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52 $chr_stats
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53 -p '$adv_output.p'
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54 $adv_output.A
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55 $adv_output.C
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56 $adv_output.X
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57 $adv_output.K
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58
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59 #for $escaped_element_identifier in $escaped_element_identifiers:
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60 '$escaped_element_identifier'
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61 #end for
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62
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63 ]]></command>
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64 <inputs>
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65 <param format="gtf" name="gffinputs" type="data" label="GTF inputs for comparison" help="" multiple="true" />
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66 <conditional name="annotation">
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67 <param label="Use Reference Annotation" name="use_ref_annotation" type="select">
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68 <option value="No">No</option>
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69 <option value="Yes">Yes</option>
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70 </param>
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71 <when value="Yes">
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72 <conditional name="ref_source">
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73 <param label="Choose the source for the reference annotation" name="ref_source_sel" type="select">
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74 <option value="cached">Locally cached</option>
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75 <option value="history">History</option>
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76 </param>
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77 <when value="cached">
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78 <param argument="-r" label="Using reference annotation" name="index" type="select">
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79 <options from_data_table="gene_sets">
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80 <!--filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" /-->
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81 </options>
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82 <validator message="No reference annotation is available for the build associated with the selected input dataset" type="no_options" />
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83 </param>
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84 </when>
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85 <when value="history">
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86 <param argument="-r" format="gff3,gtf" help="Requires an annotation file in GFF3 or GTF format." label="Reference Annotation" name="reference_annotation" type="data" />
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87 </when>
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88 </conditional>
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89 <param argument="-R" falsevalue="" help="consider only the reference transcripts that overlap any of the input transfrags (Sn correction)" label="Ignore reference transcripts that are not overlapped by any input transfrags" name="ignore_nonoverlapping_reference" truevalue="-R" type="boolean" />
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90 <param argument="-Q" falsevalue="" help="consider only the input transcripts that overlap any of the reference transcripts (Sp correction). Warning: this will discard all 'novel' loci!" label="Ignore input transcripts that are not overlapped by any reference transcripts" name="ignore_nonoverlapping_transfrags" truevalue="-Q" type="boolean" />
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91 <param argument="--strict-match" name="strict_match" type="boolean" checked="false" truevalue="--strict-match" falsevalue="" label="the match code '=' is only assigned when all exon boundaries match" help="code '~' is assigned for intron chain match or single-exon" />
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92 <param argument="-T" name="refmap_tmap" label="Generate tmap or refmap file for each input file" type="select" multiple="True">
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93 <option value="refmap" selected="True">refmap</option>
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94 <option value="tmap" selected="True">tmap</option>
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95 </param>
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96 </when>
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97 <when value="No">
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98 <param argument="-T" name="refmap_tmap" label="Generate tmap file for each input file" type="select" multiple="True">
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99 <option value="tmap" selected="True">tmap</option>
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100 </param>
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101 </when>
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102 </conditional>
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103 <conditional name="seq_data">
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104 <param help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff." label="Use Sequence Data" name="use_seq_data" type="select">
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105 <option value="No">No</option>
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106 <option value="Yes">Yes</option>
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107 </param>
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108 <when value="No"/>
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109 <when value="Yes">
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110 <conditional name="seq_source">
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111 <param label="Choose the source for the reference sequence" name="index_source" type="select">
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112 <option value="cached">Locally cached</option>
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113 <option value="history">History</option>
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114 </param>
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115 <when value="cached">
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116 <param argument="-s" label="Using reference genome" name="index" type="select">
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117 <options from_data_table="fasta_indexes">
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118 <filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" />
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119 </options>
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120 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
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121 </param>
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122 </when>
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123 <when value="history">
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124 <param argument="-s" format="fasta" label="Using reference file" name="ref_file" type="data" />
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125 </when>
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126 </conditional>
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127 </when>
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128 </conditional>
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129 <param name="discard_single_exon" argument="-M/-N" type="select" label="Discard single-exon transcripts" help="If -S and also --strict-match is given, exact matching of all exon boundaries is required">
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130 <option selected="True" value="">No</option>
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131 <option value="-M">Discard single-exon transfrags and reference transcripts</option>
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132 <option value="-N">Discard single-exon reference transcripts</option>
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133 </param>
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134 <param label="Discard duplicates" name="discard_duplicates" type="select">
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135 <option value="">None</option>
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136 <option value="-D">discard 'duplicate' query transfrags within a single sample (-D)</option>
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137 <option value="-S">Only discard 'duplicate' query or reference transcripts if their boundaries are fully contained within other, larger or identical transfrags (-S)</option>
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138 </param>
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139 <param name="no_merge" argument="--no-merge" type="boolean" checked="false" truevalue="--no-merge" falsevalue="" label="Disable close-exon merging" help="Default: merge exons separated by 'introns' shorter than 5 bases" />
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140 <param argument="-e" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" label="Max. Distance for assessing exon accuracy" name="max_dist_exon" type="integer" value="100" />
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141 <param argument="-d" help="max. distance (range) for grouping transcript start sites. Default: 100" label="Max distance for transcript grouping" name="max_dist_group" type="integer" value="100" />
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142 <param name="chr_stats" argument="--chr-stats" type="boolean" checked="false" truevalue="--chr-stats" falsevalue="" label="Show summary and accuracy data separately for each reference sequence in the transcript accuracy data set" />
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143 <section name="adv_output" title="Options for the combined GTF output file">
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144 <param argument="-p" type="text" value="TCONS" label="name prefix for consensus transcripts" help="for combined.gtf" />
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145 <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue="" label="discard matching and 'contained' transfrags" help="i.e. collapse intron-redundant transfrags across all query files" />
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146 <param argument="-A" type="boolean" checked="false" truevalue="-A" falsevalue="" label="discard the 'contained' transfrags except intron-redundant transfrags starting with a different 5' exon" help="like -C but does not discard intron-redundant transfrags if they start with a different 5' exon" />
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147 <param argument="-X" type="boolean" checked="false" truevalue="-X" falsevalue="" label="discard the 'contained' transfrags also if ends stick out within the container's introns" help="like -C but also discard contained transfrags if transfrag ends stick out within the container's introns" />
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148 <param argument="-K" type="boolean" checked="false" truevalue="-K" falsevalue="" label="do NOT discard any redundant transfrag matching a reference" help="for -C/-A/-X" />
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149 </section>
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150 </inputs>
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151 <outputs>
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152 <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" />
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153 <data format="tabular" from_work_dir="gffcmp.loci" label="${tool.name} on ${on_string}: loci" name="transcripts_loci" />
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154 <data format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: data ${gffinputs[0].hid} tracking file" name="transcripts_tracking" />
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155 <data format="gtf" from_work_dir="gffcmp.combined.gtf" label="${tool.name} on ${on_string}: combined transcripts" name="transcripts_combined">
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156 <filter>(isinstance(gffinputs, list) and len(gffinputs) > 1) or annotation['use_ref_annotation'] == "No"</filter>
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157 </data>
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158 <data format="gtf" from_work_dir="gffcmp.annotated.gtf" label="${tool.name} on ${on_string}: annotated transcripts" name="transcripts_annotated">
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159 <filter>not (isinstance(gffinputs, list) and len(gffinputs) > 1) and annotation['use_ref_annotation'] == "Yes"</filter>
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160 </data>
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161 <collection name="refmap_output" type="list" label="${tool.name} on ${on_string}: refmap">
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162 <discover_datasets pattern="gffcmp\.(?P&lt;designation&gt;.+)\.refmap" ext="tabular" />
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163 <filter>annotation['refmap_tmap'] != None and 'refmap' in annotation['refmap_tmap']</filter>
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164 </collection>
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165 <collection name="tmap_output" type="list" label="${tool.name} on ${on_string}: tmap">
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166 <discover_datasets pattern="gffcmp\.(?P&lt;designation&gt;.+)\.tmap" ext="tabular" />
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167 <filter>annotation['refmap_tmap'] != None and 'tmap' in annotation['refmap_tmap']</filter>
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168 </collection>
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169 </outputs>
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170 <tests>
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171 <!-- 2 inputs, no reference, default options -->
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172 <test expect_num_outputs="5">
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173 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
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174 <conditional name="annotation">
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175 <param name="use_ref_annotation" value="No" />
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176 </conditional>
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177 <conditional name="seq_data">
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178 <param name="use_seq_data" value="No" />
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179 </conditional>
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180 <assert_command>
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diff changeset
181 <not_has_text text="-R " />
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parents:
diff changeset
182 <not_has_text text="-Q " />
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enios
parents:
diff changeset
183 <not_has_text text="--strict-match " />
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enios
parents:
diff changeset
184 <not_has_text text="-T " />
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enios
parents:
diff changeset
185 <has_text_matching expression="^.*gffcompare((?!-s).)*$" /> <!-- since ln also has -s a more complicated regexp is needed here to check if -s is not set -->
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parents:
diff changeset
186 <not_has_text text="-M " />
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enios
parents:
diff changeset
187 <not_has_text text="-N " />
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enios
parents:
diff changeset
188 <has_text text="-e 100 " />
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enios
parents:
diff changeset
189 <has_text text="-d 100 " />
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enios
parents:
diff changeset
190 <not_has_text text="-D " />
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enios
parents:
diff changeset
191 <not_has_text text="--no-merge " />
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enios
parents:
diff changeset
192 <has_text text="-p 'TCONS' " />
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enios
parents:
diff changeset
193 <not_has_text text="-C " />
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enios
parents:
diff changeset
194 <not_has_text text="-A " />
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enios
parents:
diff changeset
195 <not_has_text text="-X " />
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enios
parents:
diff changeset
196 <not_has_text text="-K " />
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parents:
diff changeset
197 </assert_command>
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parents:
diff changeset
198 <output file="gffcompare_out1.stats" name="transcripts_stats" />
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enios
parents:
diff changeset
199 <output file="gffcompare_out1.loci" name="transcripts_loci" />
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enios
parents:
diff changeset
200 <output file="gffcompare_out1.tracking" name="transcripts_tracking" />
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enios
parents:
diff changeset
201 <output file="gffcompare_out1.gtf" name="transcripts_combined" />
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enios
parents:
diff changeset
202 <output_collection name="tmap_output" type="list" count="2"/>
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enios
parents:
diff changeset
203 </test>
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parents:
diff changeset
204 <!-- 2 inputs, no reference, with refsequence, default options (but disable tmap output) -->
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enios
parents:
diff changeset
205 <test expect_num_outputs="4">
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enios
parents:
diff changeset
206 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
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enios
parents:
diff changeset
207 <conditional name="annotation">
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enios
parents:
diff changeset
208 <param name="use_ref_annotation" value="No" />
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enios
parents:
diff changeset
209 <param name="refmap_tmap" value=""/>
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enios
parents:
diff changeset
210 </conditional>
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enios
parents:
diff changeset
211 <conditional name="seq_data">
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enios
parents:
diff changeset
212 <param name="use_seq_data" value="Yes" />
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enios
parents:
diff changeset
213 <conditional name="seq_source">
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parents:
diff changeset
214 <param name="index_source" value="history"/>
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enios
parents:
diff changeset
215 <param name="ref_file" ftype="fasta" value="sequence.fa"/>
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enios
parents:
diff changeset
216 </conditional>
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parents:
diff changeset
217 </conditional>
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parents:
diff changeset
218 <assert_command>
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parents:
diff changeset
219 <not_has_text text="-R " />
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enios
parents:
diff changeset
220 <not_has_text text="-Q " />
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enios
parents:
diff changeset
221 <has_text text="-T " />
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enios
parents:
diff changeset
222 <has_text_matching expression="gffcompare.*-s " /> <!-- since ln also has -s a more complicated regexp is needed here to check if -s is set -->
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parents:
diff changeset
223 <not_has_text text="-M " />
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enios
parents:
diff changeset
224 <not_has_text text="-N " />
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enios
parents:
diff changeset
225 <has_text text="-e 100 " />
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enios
parents:
diff changeset
226 <has_text text="-d 100 " />
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enios
parents:
diff changeset
227 <has_text text="-p 'TCONS' " />
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enios
parents:
diff changeset
228 <not_has_text text="-C " />
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enios
parents:
diff changeset
229 <not_has_text text="-A " />
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enios
parents:
diff changeset
230 <not_has_text text="-X " />
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enios
parents:
diff changeset
231 <not_has_text text="-K " />
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enios
parents:
diff changeset
232 </assert_command>
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parents:
diff changeset
233 <output file="gffcompare_out1.stats" name="transcripts_stats" compare="sim_size" />
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enios
parents:
diff changeset
234 <output file="gffcompare_out1.loci" name="transcripts_loci" compare="sim_size" />
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enios
parents:
diff changeset
235 <output file="gffcompare_out1.tracking" name="transcripts_tracking" compare="sim_size" />
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enios
parents:
diff changeset
236 <output file="gffcompare_out1.gtf" name="transcripts_combined" compare="sim_size" />
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parents:
diff changeset
237 </test>
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enios
parents:
diff changeset
238 <!-- 2 inputs, no reference, with cached refsequence, default options (but disable tmap output) -->
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enios
parents:
diff changeset
239 <test expect_num_outputs="4">
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enios
parents:
diff changeset
240 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" dbkey="hg17" />
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enios
parents:
diff changeset
241 <conditional name="annotation">
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enios
parents:
diff changeset
242 <param name="use_ref_annotation" value="No" />
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enios
parents:
diff changeset
243 <param name="refmap_tmap" value=""/>
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enios
parents:
diff changeset
244 </conditional>
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enios
parents:
diff changeset
245 <conditional name="seq_data">
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enios
parents:
diff changeset
246 <param name="use_seq_data" value="Yes" />
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enios
parents:
diff changeset
247 <conditional name="seq_source">
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enios
parents:
diff changeset
248 <param name="index_source" value="cached"/>
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enios
parents:
diff changeset
249 <param name="index" value="test_buildid"/>
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enios
parents:
diff changeset
250 </conditional>
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enios
parents:
diff changeset
251 </conditional>
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enios
parents:
diff changeset
252 <assert_command>
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enios
parents:
diff changeset
253 <not_has_text text="-R " />
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enios
parents:
diff changeset
254 <not_has_text text="-Q " />
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enios
parents:
diff changeset
255 <has_text text="-T " />
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enios
parents:
diff changeset
256 <has_text_matching expression="gffcompare.*-s " />
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enios
parents:
diff changeset
257 <not_has_text text="-M " />
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enios
parents:
diff changeset
258 <not_has_text text="-N " />
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enios
parents:
diff changeset
259 <has_text text="-e 100 " />
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enios
parents:
diff changeset
260 <has_text text="-d 100 " />
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enios
parents:
diff changeset
261 <has_text text="-p 'TCONS' " />
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enios
parents:
diff changeset
262 <not_has_text text="-C " />
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enios
parents:
diff changeset
263 <not_has_text text="-A " />
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enios
parents:
diff changeset
264 <not_has_text text="-X " />
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enios
parents:
diff changeset
265 <not_has_text text="-K " />
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enios
parents:
diff changeset
266 </assert_command>
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enios
parents:
diff changeset
267 <output file="gffcompare_out1.stats" name="transcripts_stats" compare="sim_size" />
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enios
parents:
diff changeset
268 <output file="gffcompare_out1.loci" name="transcripts_loci" compare="sim_size" />
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enios
parents:
diff changeset
269 <output file="gffcompare_out1.tracking" name="transcripts_tracking" compare="sim_size" />
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enios
parents:
diff changeset
270 <output file="gffcompare_out1.gtf" name="transcripts_combined" compare="sim_size" />
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enios
parents:
diff changeset
271 </test>
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enios
parents:
diff changeset
272 <!-- 2 inputs and reference, default options -->
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enios
parents:
diff changeset
273 <test expect_num_outputs="6">
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enios
parents:
diff changeset
274 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
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enios
parents:
diff changeset
275 <conditional name="annotation">
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enios
parents:
diff changeset
276 <param name="use_ref_annotation" value="Yes" />
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enios
parents:
diff changeset
277 <conditional name="ref_source">
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enios
parents:
diff changeset
278 <param name="ref_source_sel" value="history"/>
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enios
parents:
diff changeset
279 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />
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enios
parents:
diff changeset
280 </conditional>
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enios
parents:
diff changeset
281 </conditional>
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enios
parents:
diff changeset
282 <conditional name="seq_data">
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enios
parents:
diff changeset
283 <param name="use_seq_data" value="No" />
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enios
parents:
diff changeset
284 </conditional>
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enios
parents:
diff changeset
285 <assert_command>
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enios
parents:
diff changeset
286 <not_has_text text="-R " />
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enios
parents:
diff changeset
287 <not_has_text text="-Q " />
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enios
parents:
diff changeset
288 <not_has_text text="--strict-match " />
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enios
parents:
diff changeset
289 <not_has_text text="-T " />
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enios
parents:
diff changeset
290 <not_has_text text="-M " />
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enios
parents:
diff changeset
291 <not_has_text text="-N " />
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enios
parents:
diff changeset
292 <has_text text="-e 100 " />
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enios
parents:
diff changeset
293 <has_text text="-d 100 " />
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enios
parents:
diff changeset
294 <not_has_text text="-D " />
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enios
parents:
diff changeset
295 <not_has_text text="--no-merge " />
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enios
parents:
diff changeset
296 <not_has_text text="--chr-stats" />
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enios
parents:
diff changeset
297 <has_text text="-p 'TCONS' " />
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enios
parents:
diff changeset
298 <not_has_text text="-C " />
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enios
parents:
diff changeset
299 <not_has_text text="-A " />
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enios
parents:
diff changeset
300 <not_has_text text="-X " />
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enios
parents:
diff changeset
301 <not_has_text text="-K " />
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enios
parents:
diff changeset
302 </assert_command>
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enios
parents:
diff changeset
303 <output file="gffcompare_out2.stats" name="transcripts_stats" />
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enios
parents:
diff changeset
304 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" />
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enios
parents:
diff changeset
305 <output file="gffcompare_out2.tracking" name="transcripts_tracking" />
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enios
parents:
diff changeset
306 <output file="gffcompare_out2.gtf" name="transcripts_combined" />
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enios
parents:
diff changeset
307 <output_collection name="refmap_output" type="list" count="2">
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enios
parents:
diff changeset
308 <element name="gffcompare_in1_gtf" file="gffcompare_out2-1.refmap" ftype="tabular" />
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enios
parents:
diff changeset
309 <element name="gffcompare_in2_gtf" file="gffcompare_out2-2.refmap" ftype="tabular" />
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enios
parents:
diff changeset
310 </output_collection>
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enios
parents:
diff changeset
311 <output_collection name="tmap_output" type="list" count="2">
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enios
parents:
diff changeset
312 <element name="gffcompare_in1_gtf" file="gffcompare_out2-1.tmap" ftype="tabular" />
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enios
parents:
diff changeset
313 <element name="gffcompare_in2_gtf" file="gffcompare_out2-2.tmap" ftype="tabular" />
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enios
parents:
diff changeset
314 </output_collection>
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enios
parents:
diff changeset
315 </test>
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enios
parents:
diff changeset
316 <!-- 2 inputs and reference (cached), non default options, only refmap output -->
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enios
parents:
diff changeset
317 <test expect_num_outputs="5">
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enios
parents:
diff changeset
318 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" dbkey="hg17" />
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enios
parents:
diff changeset
319 <conditional name="annotation">
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enios
parents:
diff changeset
320 <param name="use_ref_annotation" value="Yes" />
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enios
parents:
diff changeset
321 <conditional name="ref_source">
24d0a81802d6 Uploaded
enios
parents:
diff changeset
322 <param name="ref_source_sel" value="cached"/>
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enios
parents:
diff changeset
323 <param name="index" value="test_buildid"/>
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enios
parents:
diff changeset
324 </conditional>
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enios
parents:
diff changeset
325 <param name="ignore_nonoverlapping_reference" value="Yes" />
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enios
parents:
diff changeset
326 <param name="ignore_nonoverlapping_transfrags" value="Yes" />
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enios
parents:
diff changeset
327 <param name="strict_match" value="--strict-match" />
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enios
parents:
diff changeset
328 <param name="refmap_tmap" value="refmap" />
24d0a81802d6 Uploaded
enios
parents:
diff changeset
329 </conditional>
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enios
parents:
diff changeset
330 <conditional name="seq_data">
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enios
parents:
diff changeset
331 <param name="use_seq_data" value="No" />
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enios
parents:
diff changeset
332 </conditional>
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enios
parents:
diff changeset
333 <param name="discard_single_exon" value="-M"/>
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enios
parents:
diff changeset
334 <param name="discard_duplicates" value="-D"/>
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enios
parents:
diff changeset
335 <param name="no_merge" value="--no-merge" />
24d0a81802d6 Uploaded
enios
parents:
diff changeset
336 <param name="max_dist_exon" value="101" />
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enios
parents:
diff changeset
337 <param name="max_dist_group" value="99" />
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enios
parents:
diff changeset
338 <param name="chr_stats" value="--chr-stats" />
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enios
parents:
diff changeset
339 <assert_command>
24d0a81802d6 Uploaded
enios
parents:
diff changeset
340 <has_text text="-R " />
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enios
parents:
diff changeset
341 <has_text text="-Q " />
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enios
parents:
diff changeset
342 <has_text text="--strict-match " />
24d0a81802d6 Uploaded
enios
parents:
diff changeset
343 <not_has_text text="-T " />
24d0a81802d6 Uploaded
enios
parents:
diff changeset
344 <has_text text="-M " />
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enios
parents:
diff changeset
345 <not_has_text text="-N " />
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enios
parents:
diff changeset
346 <has_text text="-e 101 " />
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enios
parents:
diff changeset
347 <has_text text="-d 99 " />
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enios
parents:
diff changeset
348 <has_text text="-D " />
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enios
parents:
diff changeset
349 <has_text text="--no-merge " />
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enios
parents:
diff changeset
350 <has_text text="--chr-stats" />
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enios
parents:
diff changeset
351 <has_text text="-p 'TCONS' " />
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enios
parents:
diff changeset
352 <not_has_text text="-C " />
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enios
parents:
diff changeset
353 <not_has_text text="-A " />
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enios
parents:
diff changeset
354 <not_has_text text="-X " />
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enios
parents:
diff changeset
355 <not_has_text text="-K " />
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enios
parents:
diff changeset
356 </assert_command>
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enios
parents:
diff changeset
357 <output file="gffcompare_out2.stats" name="transcripts_stats" compare="sim_size" />
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enios
parents:
diff changeset
358 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" />
24d0a81802d6 Uploaded
enios
parents:
diff changeset
359 <output file="gffcompare_out2.tracking" name="transcripts_tracking" compare="sim_size" />
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enios
parents:
diff changeset
360 <output file="gffcompare_out2.gtf" name="transcripts_combined" compare="sim_size" delta="50000"/>
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enios
parents:
diff changeset
361 <output_collection name="refmap_output" type="list" count="0"/> <!-- because of -M no refmaps are created -->
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enios
parents:
diff changeset
362 </test>
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enios
parents:
diff changeset
363 <!-- 2 inputs and reference, non default advanced options, only tmap output -->
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enios
parents:
diff changeset
364 <test expect_num_outputs="5">
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enios
parents:
diff changeset
365 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
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enios
parents:
diff changeset
366 <conditional name="annotation">
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enios
parents:
diff changeset
367 <param name="use_ref_annotation" value="Yes" />
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enios
parents:
diff changeset
368 <conditional name="ref_source">
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enios
parents:
diff changeset
369 <param name="ref_source_sel" value="history"/>
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enios
parents:
diff changeset
370 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />
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371 </conditional>
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372 <param name="refmap_tmap" value="tmap" />
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373 </conditional>
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374 <conditional name="seq_data">
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375 <param name="use_seq_data" value="No" />
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376 </conditional>
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377 <section name="adv_output">
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378 <param name="p" value="OTHER" />
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379 <param name="C" value="-C" />
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380 <param name="A" value="-A" />
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381 <param name="X" value="-X" />
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382 <param name="K" value="-K" />
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383 </section>
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384 <assert_command>
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385 <not_has_text text="-R " />
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386 <not_has_text text="-Q " />
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387 <not_has_text text="--strict-match " />
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388 <not_has_text text="-T " />
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389 <not_has_text text="-M " />
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390 <not_has_text text="-N " />
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parents:
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391 <has_text text="-e 100 " />
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392 <has_text text="-d 100 " />
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393 <not_has_text text="-D " />
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394 <not_has_text text="--no-merge " />
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395 <not_has_text text="--chr-stats" />
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396 <has_text text="-p 'OTHER' " />
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397 <has_text text="-C " />
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398 <has_text text="-A " />
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399 <has_text text="-X " />
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400 <has_text text="-K " />
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401 </assert_command>
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402 <output file="gffcompare_out2.stats" name="transcripts_stats" compare="sim_size" />
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403 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" />
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404 <output file="gffcompare_out2.tracking" name="transcripts_tracking" compare="sim_size" />
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405 <output file="gffcompare_out2.gtf" name="transcripts_combined" compare="sim_size" delta="50000"/>
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406 <output_collection name="tmap_output" type="list" count="2"/>
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407 </test>
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408 <!-- 2 inputs and reference, default options, no tmap or refmap output -->
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409 <test expect_num_outputs="4">
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410 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
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411 <conditional name="annotation">
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412 <param name="use_ref_annotation" value="Yes" />
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413 <conditional name="ref_source">
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414 <param name="ref_source_sel" value="history"/>
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415 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />
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416 </conditional>
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417 <param name="refmap_tmap" value="" />
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418 </conditional>
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419 <conditional name="seq_data">
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420 <param name="use_seq_data" value="No" />
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421 </conditional>
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422 <assert_command>
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423 <not_has_text text="-R " />
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424 <not_has_text text="-Q " />
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425 <not_has_text text="--strict-match " />
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426 <has_text text="-T " />
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parents:
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427 <not_has_text text="-M " />
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428 <not_has_text text="-N " />
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parents:
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429 <has_text text="-e 100 " />
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parents:
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430 <has_text text="-d 100 " />
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parents:
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431 <not_has_text text="-D " />
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432 <not_has_text text="--no-merge " />
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433 <not_has_text text="--chr-stats" />
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parents:
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434 <has_text text="-p 'TCONS' " />
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parents:
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435 <not_has_text text="-C " />
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parents:
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436 <not_has_text text="-A " />
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parents:
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437 <not_has_text text="-X " />
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parents:
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438 <not_has_text text="-K " />
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439 </assert_command>
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440 <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="2" />
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parents:
diff changeset
441 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" />
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parents:
diff changeset
442 <output file="gffcompare_out2.tracking" name="transcripts_tracking" />
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parents:
diff changeset
443 <output file="gffcompare_out2.gtf" name="transcripts_combined" />
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parents:
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444 </test>
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445
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446 <test expect_num_outputs="4">
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parents:
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447 <param ftype="gtf" name="gffinputs" value="gffcompare_in4.gtf" />
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parents:
diff changeset
448 <conditional name="annotation">
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parents:
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449 <param name="use_ref_annotation" value="Yes" />
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parents:
diff changeset
450 <conditional name="ref_source">
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parents:
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451 <param name="ref_source_sel" value="history"/>
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parents:
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452 <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" />
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parents:
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453 </conditional>
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parents:
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454 <param name="ignore_nonoverlapping_reference" value="Yes" />
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parents:
diff changeset
455 <param name="ignore_nonoverlapping_transfrags" value="No" />
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parents:
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456 <param name="refmap_tmap" value="" />
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457 </conditional>
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parents:
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458 <param name="use_seq_data" value="No" />
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parents:
diff changeset
459 <param name="discard_single_exon" value="" />
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parents:
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460 <param name="max_dist_exon" value="100" />
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parents:
diff changeset
461 <param name="max_dist_group" value="100" />
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parents:
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462 <output file="gffcompare_out3.stats" name="transcripts_stats"/>
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parents:
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463 <output file="gffcompare_out3.loci" name="transcripts_loci" compare="sim_size" />
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parents:
diff changeset
464 <output file="gffcompare_out3.tracking" name="transcripts_tracking" />
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parents:
diff changeset
465 <output file="gffcompare_out3.gtf" name="transcripts_annotated" />
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parents:
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466 </test>
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467 </tests>
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parents:
diff changeset
468 <help>
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parents:
diff changeset
469 <![CDATA[
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parents:
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470 **GffCompare Overview**
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parents:
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471
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parents:
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472 ## GffCompare
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parents:
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473 * compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie).
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parents:
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474 * collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples)
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parents:
diff changeset
475 * classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a
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parents:
diff changeset
476 annotation file (also in GTF/GFF3 format)
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parents:
diff changeset
477
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parents:
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478 More information can be found here: https://ccb.jhu.edu/software/stringtie/gffcompare.shtml.
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parents:
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479
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480 The original form of this program is also distributed as part of the Cufflinks suite, under the name "CuffCompare"
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parents:
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481 (see manual: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/). Most of the options and parameters of CuffCompare
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parents:
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482 are supported by GffCompare, while new features will likely be added to GffCompare in the future.
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parents:
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483
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parents:
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484 A notable difference of GffCompare is that when a single query GTF/GFF file is given as input, along with a reference annotation (-r option),
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parents:
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485 gffcompare switches into "annotation mode" and it generates a .annotated.gtf file instead of the .merged.gtf produced by CuffCompare with the
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parents:
diff changeset
486 same parameters. This file has the same general format as CuffCompare's .merged.gtf file (with "class codes" assigned to transcripts as per
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parents:
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487 their relationship with the matching/overlapping reference transcript), but the original transcript IDs are preserved, so gffcompare can thus
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parents:
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488 be used as a simple way of annotating a set of transcripts.
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parents:
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489
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parents:
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490 Another important difference is that the input transcripts are no longer discarded when they are found to be "intron redundant", i.e.
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parents:
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491 contained within other, longer isoforms. CuffCompare had the -G option to prevent collapsing of such intron redundant isoforms into
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parents:
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492 their longer "containers", but GffCompare has made this the default mode of operation (hence the -G option is no longer needed
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parents:
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493 and is simply ignored when given).
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parents:
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494 ]]>
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parents:
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495 </help>
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parents:
diff changeset
496 <citations>
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parents:
diff changeset
497 <citation type="doi">10.1038/nbt.1621</citation>
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parents:
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498 </citations>
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499 </tool>