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annotate gffcompare.xml @ 3:2bb86e2c417f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
author iuc
date Mon, 27 May 2019 13:54:15 -0400
parents f99d7825a501
children 0f710191a66d
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2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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1 <tool id="gffcompare" name="GffCompare" version="@GFFCOMPARE_VERSION@">
0
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2 <description>compare assembled transcripts to a reference annotation</description>
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3 <macros>
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4 <token name="@GFFCOMPARE_VERSION@">0.11.2</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@GFFCOMPARE_VERSION@">gffcompare</requirement>
0
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8 </requirements>
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9 <version_command>gffcompare -v | awk '{print $2}'</version_command>
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10 <command detect_errors="aggressive"><![CDATA[
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11 #import re
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12
1
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13 #set escaped_element_identifiers = [re.sub('[^\w\-]', '_', str(_.element_identifier)) for _ in $gffinputs]
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14 #for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers):
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15 ln -s '$input' '$escaped_element_identifier' &&
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16 #end for
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17 #if $seq_data.use_seq_data == "Yes":
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18 #if $seq_data.seq_source.index_source == "history":
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19 ln -s '$seq_data.seq_source.ref_file' ref_seq.fa &&
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20 #else:
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21 ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa &&
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22 #end if
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23 #end if
0
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24
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25 #if $annotation.use_ref_annotation == "Yes":
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26 #if $annotation.ref_source.ref_source_sel == "history":
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27 ln -s '$annotation.ref_source.reference_annotation' ref_annotation &&
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28 #else
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29 ln -s '$annotation.ref_source.index.fields.path' ref_annotation &&
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30 #end if
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31 #end if
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32
1
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33 gffcompare
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34 ## Use annotation reference?
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35 #if $annotation.use_ref_annotation == "Yes":
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36 -r ref_annotation
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37 $annotation.ignore_nonoverlapping_reference
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38 $annotation.ignore_nonoverlapping_transfrags
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39 $annotation.strict_match
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40 #end if
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41 #if $annotation.refmap_tmap == "":
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42 -T
1
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43 #end if
0
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44
1
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45 ## Use sequence data?
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46 #if $seq_data.use_seq_data == "Yes":
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47 -s ref_seq.fa
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48 #end if
0
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49
1
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50 $discard_single_exon
3
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51 $discard_duplicates
1
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52 -e $max_dist_exon
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53 -d $max_dist_group
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54 $chr_stats
2
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55 -p '$adv_output.p'
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56 $adv_output.A
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57 $adv_output.C
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58 $adv_output.X
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59 $adv_output.K
1
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60
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61 #for $escaped_element_identifier in $escaped_element_identifiers:
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62 '$escaped_element_identifier'
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63 #end for
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64
1
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65 ]]></command>
0
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66 <inputs>
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67 <param format="gtf" name="gffinputs" type="data" label="GTF inputs for comparison" help="" multiple="true" />
0
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68 <conditional name="annotation">
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69 <param label="Use Reference Annotation" name="use_ref_annotation" type="select">
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70 <option value="No">No</option>
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71 <option value="Yes">Yes</option>
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72 </param>
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73 <when value="Yes">
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74 <conditional name="ref_source">
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75 <param label="Choose the source for the reference annotation" name="ref_source_sel" type="select">
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76 <option value="cached">Locally cached</option>
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77 <option value="history">History</option>
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78 </param>
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79 <when value="cached">
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80 <param argument="-r" label="Using reference annotation" name="index" type="select">
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81 <options from_data_table="gene_sets">
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82 <filter column="1" key="dbkey" ref="gffinputs" type="data_meta" />
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83 </options>
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84 <validator message="No reference annotation is available for the build associated with the selected input dataset" type="no_options" />
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85 </param>
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86 </when>
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87 <when value="history">
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88 <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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89 </when>
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90 </conditional>
0
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91 <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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92 <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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93 <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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94 <param argument="-T" name="refmap_tmap" label="Generate tmap or refmap file for each input file" type="select" multiple="True">
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95 <option value="refmap" selected="True">refmap</option>
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96 <option value="tmap" selected="True">tmap</option>
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97 </param>
0
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98 </when>
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99 <when value="No">
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100 <param argument="-T" name="refmap_tmap" label="Generate tmap file for each input file" type="select" multiple="True">
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101 <option value="tmap" selected="True">tmap</option>
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102 </param>
0
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103 </when>
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104 </conditional>
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105 <conditional name="seq_data">
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106 <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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107 <option value="No">No</option>
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108 <option value="Yes">Yes</option>
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109 </param>
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110 <when value="No"/>
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111 <when value="Yes">
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112 <conditional name="seq_source">
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113 <param label="Choose the source for the reference sequence" name="index_source" type="select">
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114 <option value="cached">Locally cached</option>
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115 <option value="history">History</option>
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116 </param>
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117 <when value="cached">
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118 <param argument="-s" label="Using reference genome" name="index" type="select">
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119 <options from_data_table="fasta_indexes">
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120 <filter column="1" key="dbkey" ref="gffinputs" type="data_meta" />
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121 </options>
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122 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
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123 </param>
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124 </when>
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125 <when value="history">
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126 <param argument="-s" format="fasta" label="Using reference file" name="ref_file" type="data" />
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127 </when>
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128 </conditional>
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129 </when>
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130 </conditional>
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131 <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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132 <option selected="True" value="">No</option>
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133 <option value="-M">Discard single-exon transfrags and reference transcripts</option>
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134 <option value="-N">Discard single-exon reference transcripts</option>
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135 </param>
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136 <param label="Discard duplicates" name="discard_duplicates" type="select">
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137 <option value="">None</option>
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138 <option value="-D">discard 'duplicate' query transfrags within a single sample (-D)</option>
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139 <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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140 </param>
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141 <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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142 <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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143 <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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144 <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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145 <section name="adv_output" title="Options for the combined GTF output file">
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146 <param argument="-p" type="text" value="TCONS" label="name prefix for consensus transcripts" help="for combined.gtf (default: 'TCONS')" />
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147 <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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148 <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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149 <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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150 <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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151 </section>
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152 </inputs>
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153 <outputs>
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154 <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" />
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155 <data format="tabular" from_work_dir="gffcmp.loci" label="${tool.name} on ${on_string}: loci" name="transcripts_loci" />
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156 <data format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: data ${gffinputs[0].hid} tracking file" name="transcripts_tracking" />
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157 <data format="gtf" from_work_dir="gffcmp.combined.gtf" label="${tool.name} on ${on_string}: combined transcripts" name="transcripts_combined">
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158 <filter>(isinstance(gffinputs, list) and len(gffinputs) > 1) or annotation['use_ref_annotation'] == "No"</filter>
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159 </data>
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160 <data format="gtf" from_work_dir="gffcmp.annotated.gtf" label="${tool.name} on ${on_string}: annotated transcripts" name="transcripts_annotated">
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161 <filter>not (isinstance(gffinputs, list) and len(gffinputs) > 1) and annotation['use_ref_annotation'] == "Yes"</filter>
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162 </data>
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163 <collection name="refmap_output" type="list" label="${tool.name} on ${on_string}: refmap">
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164 <discover_datasets pattern="gffcmp\.(?P&lt;designation&gt;.+)\.refmap" ext="tabular" />
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165 <filter>annotation['refmap_tmap'] != None and 'refmap' in annotation['refmap_tmap']</filter>
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166 </collection>
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167 <collection name="tmap_output" type="list" label="${tool.name} on ${on_string}: tmap">
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168 <discover_datasets pattern="gffcmp\.(?P&lt;designation&gt;.+)\.tmap" ext="tabular" />
3
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169 <filter>annotation['refmap_tmap'] != None and 'tmap' in annotation['refmap_tmap']</filter>
1
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170 </collection>
0
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171 </outputs>
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172 <tests>
3
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173 <!-- 2 inputs, no reference, default options -->
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174 <test expect_num_outputs="5">
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175 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
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176 <conditional name="annotation">
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177 <param name="use_ref_annotation" value="No" />
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178 </conditional>
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179 <conditional name="seq_data">
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180 <param name="use_seq_data" value="No" />
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181 </conditional>
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182 <assert_command>
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183 <not_has_text text="-R " />
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184 <not_has_text text="-Q " />
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185 <not_has_text text="--strict-match " />
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186 <not_has_text text="-T " />
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187 <not_has_text text="-s " />
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188 <not_has_text text="-M " />
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189 <not_has_text text="-N " />
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190 <has_text text="-e 100 " />
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191 <has_text text="-d 100 " />
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192 <not_has_text text="-D " />
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193 <not_has_text text="--no-merge " />
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194 <has_text text="-p TCONS " />
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195 <not_has_text text="-C " />
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196 <not_has_text text="-A " />
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197 <not_has_text text="-X " />
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198 <not_has_text text="-K " />
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199 </assert_command>
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200 <output file="gffcompare_out1.stats" name="transcripts_stats" />
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201 <output file="gffcompare_out1.loci" name="transcripts_loci" />
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202 <output file="gffcompare_out1.tracking" name="transcripts_tracking" />
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203 <output file="gffcompare_out1.gtf" name="transcripts_combined" />
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204 <output_collection name="tmap_output" type="list" count="2"/>
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205 </test>
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206 <!-- 2 inputs, no reference, with refsequence, default options (but disable tmap output) -->
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207 <test expect_num_outputs="4">
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208 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
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209 <conditional name="annotation">
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210 <param name="use_ref_annotation" value="No" />
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211 <param name="refmap_tmap" value=""/>
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212 </conditional>
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213 <conditional name="seq_data">
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214 <param name="use_seq_data" value="Yes" />
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215 <conditional name="seq_source">
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216 <param name="index_source" value="history"/>
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217 <param name="ref_file" ftype="fasta" value="sequence.fa"/>
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218 </conditional>
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219 </conditional>
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220 <assert_command>
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221 <not_has_text text="-R " />
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222 <not_has_text text="-Q " />
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223 <has_text text="-T " />
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224 <has_text text="-s " />
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225 <not_has_text text="-M " />
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226 <not_has_text text="-N " />
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227 <has_text text="-e 100 " />
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228 <has_text text="-d 100 " />
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229 <has_text text="-p TCONS " />
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230 <not_has_text text="-C " />
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231 <not_has_text text="-A " />
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232 <not_has_text text="-X " />
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233 <not_has_text text="-K " />
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234 </assert_command>
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235 <output file="gffcompare_out1.stats" name="transcripts_stats" compare="sim_size" />
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236 <output file="gffcompare_out1.loci" name="transcripts_loci" compare="sim_size" />
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237 <output file="gffcompare_out1.tracking" name="transcripts_tracking" compare="sim_size" />
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238 <output file="gffcompare_out1.gtf" name="transcripts_combined" compare="sim_size" />
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239 </test>
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240 <!-- 2 inputs, no reference, with cached refsequence, default options (but disable tmap output) -->
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241 <test expect_num_outputs="4">
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242 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" dbkey="hg17" />
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243 <conditional name="annotation">
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244 <param name="use_ref_annotation" value="No" />
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245 <param name="refmap_tmap" value=""/>
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246 </conditional>
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247 <conditional name="seq_data">
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248 <param name="use_seq_data" value="Yes" />
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249 <conditional name="seq_source">
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250 <param name="index_source" value="cached"/>
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251 <param name="index" value="test_buildid"/>
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252 </conditional>
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253 </conditional>
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254 <assert_command>
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255 <not_has_text text="-R " />
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256 <not_has_text text="-Q " />
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257 <has_text text="-T " />
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258 <has_text text="-s " />
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259 <not_has_text text="-M " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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260 <not_has_text text="-N " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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261 <has_text text="-e 100 " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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262 <has_text text="-d 100 " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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263 <has_text text="-p TCONS " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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264 <not_has_text text="-C " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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265 <not_has_text text="-A " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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266 <not_has_text text="-X " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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267 <not_has_text text="-K " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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268 </assert_command>
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269 <output file="gffcompare_out1.stats" name="transcripts_stats" compare="sim_size" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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270 <output file="gffcompare_out1.loci" name="transcripts_loci" compare="sim_size" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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271 <output file="gffcompare_out1.tracking" name="transcripts_tracking" compare="sim_size" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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272 <output file="gffcompare_out1.gtf" name="transcripts_combined" compare="sim_size" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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273 </test>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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274 <!-- 2 inputs and reference, default options -->
1
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275 <test expect_num_outputs="6">
c80cdc2eac6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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276 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
c80cdc2eac6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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277 <conditional name="annotation">
3
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278 <param name="use_ref_annotation" value="Yes" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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279 <conditional name="ref_source">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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280 <param name="ref_source_sel" value="history"/>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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281 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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282 </conditional>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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283 </conditional>
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284 <conditional name="seq_data">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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285 <param name="use_seq_data" value="No" />
1
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286 </conditional>
3
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287 <assert_command>
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288 <not_has_text text="-R " />
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289 <not_has_text text="-Q " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff changeset
290 <not_has_text text="-T " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff changeset
291 <not_has_text text="-M " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff changeset
292 <not_has_text text="-N " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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293 <has_text text="-e 100 " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff changeset
294 <has_text text="-d 100 " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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295 <has_text text="-p TCONS " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff changeset
296 <not_has_text text="-C " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff changeset
297 <not_has_text text="-A " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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298 <not_has_text text="-X " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff changeset
299 <not_has_text text="-K " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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300 </assert_command>
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iuc
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301 <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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302 <output file="gffcompare_out2.loci" name="transcripts_loci" lines_diff="2" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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303 <output file="gffcompare_out2.tracking" name="transcripts_tracking" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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304 <output file="gffcompare_out2.gtf" name="transcripts_combined" />
1
c80cdc2eac6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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305 <output_collection name="refmap_output" type="list" count="2">
3
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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306 <element name="gffcompare_in1_gtf" file="gffcompare_out2-1.refmap" ftype="tabular" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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307 <element name="gffcompare_in2_gtf" file="gffcompare_out2-2.refmap" ftype="tabular" />
1
c80cdc2eac6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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308 </output_collection>
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309 <output_collection name="tmap_output" type="list" count="2">
3
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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310 <element name="gffcompare_in1_gtf" file="gffcompare_out2-1.tmap" ftype="tabular" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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311 <element name="gffcompare_in2_gtf" file="gffcompare_out2-2.tmap" ftype="tabular" />
1
c80cdc2eac6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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312 </output_collection>
0
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
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313 </test>
3
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314 <!-- 2 inputs and reference (cached), non default options, only refmap output -->
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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315 <test expect_num_outputs="5">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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316 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" dbkey="hg17" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff changeset
317 <conditional name="annotation">
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318 <param name="use_ref_annotation" value="Yes" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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319 <conditional name="ref_source">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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320 <param name="ref_source_sel" value="cached"/>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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321 <param name="index" value="test_buildid"/>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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322 </conditional>
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iuc
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323 <param name="ignore_nonoverlapping_reference" value="Yes" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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324 <param name="ignore_nonoverlapping_transfrags" value="Yes" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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325 <param name="strict_match" value="--strict-match" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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326 <param name="refmap_tmap" value="refmap" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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327 </conditional>
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328 <conditional name="seq_data">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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329 <param name="use_seq_data" value="No" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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330 </conditional>
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331 <param name="discard_single_exon" value="-M"/>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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332 <param name="discard_duplicates" value="-D"/>
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333 <param name="no_merge" value="--no-merge" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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334 <param name="max_dist_exon" value="101" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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335 <param name="max_dist_group" value="99" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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336 <param name="chr_stats" value="--chr-stats" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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337 <assert_command>
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diff changeset
338 <has_text text="-R " />
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diff changeset
339 <has_text text="-Q " />
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340 <has_text text="--strict-match " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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341 <not_has_text text="-T " />
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parents: 2
diff changeset
342 <has_text text="-M " />
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diff changeset
343 <not_has_text text="-N " />
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diff changeset
344 <has_text text="-e 101 " />
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345 <has_text text="-d 99 " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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diff changeset
346 <has_text text="-D " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
347 <has_text text="--no-merge " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
348 <has_text text="--chr-stats" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
349 <not_has_text text="-p TCONS " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
350 <not_has_text text="-C " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
351 <not_has_text text="-A " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
352 <not_has_text text="-X " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
353 <not_has_text text="-K " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
354 </assert_command>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
355 <output file="gffcompare_out2.stats" name="transcripts_stats" compare="sim_size" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
356 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
357 <output file="gffcompare_out2.tracking" name="transcripts_tracking" compare="sim_size" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
358 <output file="gffcompare_out2.gtf" name="transcripts_combined" compare="sim_size" delta="50000"/>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
359 <output_collection name="refmap_output" type="list" count="0"/> <!-- because of -M no refmaps are created -->
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
360 </test>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
361 <!-- 2 inputs and reference, non default advanced options, only tmap output -->
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
362 <test expect_num_outputs="5">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
363 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
364 <conditional name="annotation">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
365 <param name="use_ref_annotation" value="Yes" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
366 <conditional name="ref_source">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
367 <param name="ref_source_sel" value="history"/>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
368 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
369 </conditional>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
370 <param name="refmap_tmap" value="tmap" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
371 </conditional>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
372 <conditional name="seq_data">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
373 <param name="use_seq_data" value="No" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
374 </conditional>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
375 <section name="adv_output">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
376 <param name="p" value="OTHER" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
377 <param name="C" value="-C" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
378 <param name="A" value="-A" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
379 <param name="X" value="-X" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
380 <param name="K" value="-K" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
381 </section>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
382 <assert_command>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
383 <not_has_text text="-R " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
384 <not_has_text text="-Q " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
385 <not_has_text text="-T " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
386 <not_has_text text="-M " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
387 <not_has_text text="-N " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
388 <has_text text="-e 100 " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
389 <has_text text="-d 100 " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
390 <has_text text="-p OTHER " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
391 <has_text text="-C " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
392 <has_text text="-A " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
393 <has_text text="-X " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
394 <has_text text="-K " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
395 </assert_command>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
396 <output file="gffcompare_out2.stats" name="transcripts_stats" compare="sim_size" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
397 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
398 <output file="gffcompare_out2.tracking" name="transcripts_tracking" compare="sim_size" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
399 <output file="gffcompare_out2.gtf" name="transcripts_combined" compare="sim_size" delta="50000"/>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
400 <output_collection name="tmap_output" type="list" count="2"/>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
401 </test>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
402 <!-- 2 inputs and reference, default options, no tmap or refmap output -->
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
403 <test expect_num_outputs="4">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
404 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
405 <conditional name="annotation">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
406 <param name="use_ref_annotation" value="Yes" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
407 <conditional name="ref_source">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
408 <param name="ref_source_sel" value="history"/>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
409 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
410 </conditional>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
411 <param name="refmap_tmap" value="" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
412 </conditional>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
413 <conditional name="seq_data">
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
414 <param name="use_seq_data" value="No" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
415 </conditional>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
416 <assert_command>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
417 <not_has_text text="-R " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
418 <not_has_text text="-Q " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
419 <has_text text="-T " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
420 <not_has_text text="-M " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
421 <not_has_text text="-N " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
422 <has_text text="-e 100 " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
423 <has_text text="-d 100 " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
424 <has_text text="-p TCONS " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
425 <not_has_text text="-C " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
426 <not_has_text text="-A " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
427 <not_has_text text="-X " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
428 <not_has_text text="-K " />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
429 </assert_command>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
430 <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
431 <output file="gffcompare_out2.loci" name="transcripts_loci" lines_diff="2" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
432 <output file="gffcompare_out2.tracking" name="transcripts_tracking" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
433 <output file="gffcompare_out2.gtf" name="transcripts_combined" />
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
434 </test>
2bb86e2c417f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents: 2
diff changeset
435
1
c80cdc2eac6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 0
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436 <test expect_num_outputs="4">
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437 <param ftype="gtf" name="gffinputs" value="gffcompare_in4.gtf" />
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438 <conditional name="annotation">
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439 <param name="use_ref_annotation" value="Yes" />
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440 <conditional name="ref_source">
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441 <param name="ref_source_sel" value="history"/>
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442 <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" />
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443 </conditional>
1
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444 <param name="ignore_nonoverlapping_reference" value="Yes" />
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445 <param name="ignore_nonoverlapping_transfrags" value="No" />
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446 <param name="refmap_tmap" value="" />
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447 </conditional>
0
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448 <param name="use_seq_data" value="No" />
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449 <param name="discard_single_exon" value="" />
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450 <param name="max_dist_exon" value="100" />
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451 <param name="max_dist_group" value="100" />
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452 <output file="gffcompare_out3.stats" name="transcripts_stats" lines_diff="6" />
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453 <output file="gffcompare_out3.loci" name="transcripts_loci" />
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454 <output file="gffcompare_out3.tracking" name="transcripts_tracking" />
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455 <output file="gffcompare_out3.gtf" name="transcripts_annotated" />
0
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456 </test>
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457 </tests>
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458 <help>
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459 <![CDATA[
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460 **GffCompare Overview**
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461
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462 ## GffCompare
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463 * compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie).
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464 * collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples)
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465 * classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a
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466 annotation file (also in GTF/GFF3 format)
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467
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468 More information can be found here: https://ccb.jhu.edu/software/stringtie/gffcompare.shtml.
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469
0
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470 The original form of this program is also distributed as part of the Cufflinks suite, under the name "CuffCompare"
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471 (see manual: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/). Most of the options and parameters of CuffCompare
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472 are supported by GffCompare, while new features will likely be added to GffCompare in the future.
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473
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474 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),
0
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475 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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476 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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477 their relationship with the matching/overlapping reference transcript), but the original transcript IDs are preserved, so gffcompare can thus
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478 be used as a simple way of annotating a set of transcripts.
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479
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480 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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481 contained within other, longer isoforms. CuffCompare had the -G option to prevent collapsing of such intron redundant isoforms into
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482 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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483 and is simply ignored when given).
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484 ]]>
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485 </help>
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486 <citations>
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487 <citation type="doi">10.1038/nbt.1621</citation>
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488 </citations>
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489 </tool>