annotate gffcompare.xml @ 2:f99d7825a501 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d
author iuc
date Tue, 05 Feb 2019 15:51:44 -0500
parents c80cdc2eac6d
children 2bb86e2c417f
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1 <tool id="gffcompare" name="GffCompare" version="0.10.6">
0
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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 <requirement type="package" version="0.10.6">gffcompare</requirement>
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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 #set escaped_element_identifiers = [re.sub('[^\w\-]', '_', str(_.element_identifier)) for _ in $gffinputs]
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10 #for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers):
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11 ln -s '$input' '$escaped_element_identifier' &&
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12 #end for
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13 #if $seq_data.use_seq_data == "Yes":
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14 #if $seq_data.seq_source.index_source == "history":
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15 ln -s '$seq_data.seq_source.ref_file' ref_seq.fa &&
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16 #else:
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17 ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa &&
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18 #end if
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19 #end if
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20
1
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21 gffcompare
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22 ## Use annotation reference?
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23 #if $annotation.use_ref_annotation == "Yes":
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24 -r '$annotation.reference_annotation'
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25 $annotation.ignore_nonoverlapping_reference
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26 $annotation.ignore_nonoverlapping_transfrags
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27 #if not $annotation.refmap_tmap:
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28 -T
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29 #end if
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30 #end if
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31
1
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32 ## Use sequence data?
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33 #if $seq_data.use_seq_data == "Yes":
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34 -s ref_seq.fa
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35 #end if
0
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36
1
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37 $discard_single_exon
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38 -e $max_dist_exon
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39 -d $max_dist_group
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40 -p '$adv_output.p'
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41 $adv_output.A
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42 $adv_output.C
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43 $adv_output.X
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44 $adv_output.K
1
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45
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46 #for $escaped_element_identifier in $escaped_element_identifiers:
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47 '$escaped_element_identifier'
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48 #end for
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49
1
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50 ]]></command>
0
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51 <inputs>
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52 <param format="gtf" name="gffinputs" type="data" label="GTF inputs for comparison" help="" multiple="true" />
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53 <conditional name="annotation">
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54 <param label="Use Reference Annotation" name="use_ref_annotation" type="select">
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55 <option value="No">No</option>
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56 <option value="Yes">Yes</option>
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57 </param>
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58 <when value="Yes">
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59 <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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60 <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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61 <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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62 <param argument="-T" name="refmap_tmap" label="Generate tmap and refmap files for each input file" type="select" multiple="True">
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63 <option value="refmap" selected="True">refmap</option>
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64 <option value="tmap" selected="True">tmap</option>
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65 </param>
0
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66 </when>
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67 <when value="No">
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68 </when>
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69 </conditional>
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70 <conditional name="seq_data">
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71 <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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72 <option value="Yes">Yes</option>
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73 <option value="No">No</option>
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74 </param>
1
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75 <when value="No"/>
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76 <when value="Yes">
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77 <conditional name="seq_source">
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78 <param label="Choose the source for the reference list" name="index_source" type="select">
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79 <option value="cached">Locally cached</option>
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80 <option value="history">History</option>
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81 </param>
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82 <when value="cached">
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83 <param argument="-s" label="Using reference genome" name="index" type="select">
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84 <options from_data_table="fasta_indexes">
1
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85 <filter column="1" key="dbkey" ref="gffinputs" type="data_meta" />
0
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86 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
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87 </options>
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88 </param>
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89 </when>
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90 <when value="history">
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91 <param argument="-s" format="fasta" label="Using reference file" name="ref_file" type="data" />
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92 </when>
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93 </conditional>
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94 </when>
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95 </conditional>
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96 <param argument="-M/-N" label="discard (ignore) single-exon transcripts" name="discard_single_exon" type="select">
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97 <option selected="True" value="">No</option>
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98 <option value="-M">Discard single-exon transfrags and reference transcripts</option>
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99 <option value="-N">Discard single-exon reference transcripts</option>
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100 </param>
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101 <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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102 <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" />
2
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103 <section name="adv_output" title="Options for the annotated/combined GTF output file">
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104 <param argument="-p" type="text" value="TCONS" label="name prefix for consensus transcripts" help="for combined.gtf (default: 'TCONS')" />
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105 <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue="" label="discard the 'contained' transfrags" help="i.e. collapse intron-redundant transfrags across all query files" />
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106 <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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107 <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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108 <param argument="-K" type="boolean" checked="false" truevalue="-A" falsevalue="" label="do NOT discard any redundant transfrag matching a reference" help="for -C/-A/-X" />
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109 </section>
0
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110 </inputs>
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111 <outputs>
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112 <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" />
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113 <data format="tabular" from_work_dir="gffcmp.loci" label="${tool.name} on ${on_string}: loci" name="transcripts_loci" />
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114 <data format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: data ${gffinputs[0].hid} tracking file" name="transcripts_tracking" />
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115 <data format="gtf" from_work_dir="gffcmp.combined.gtf" label="${tool.name} on ${on_string}: combined transcripts" name="transcripts_combined">
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116 <filter>isinstance(gffinputs, list)</filter>
0
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117 </data>
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118 <data format="gtf" from_work_dir="gffcmp.annotated.gtf" label="${tool.name} on ${on_string}: annotated transcripts" name="transcripts_annotated">
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119 <filter>not isinstance(gffinputs, list)</filter>
0
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120 </data>
1
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121 <collection name="refmap_output" type="list" label="${tool.name} on ${on_string}: refmap">
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122 <discover_datasets pattern="gffcmp\.(?P&lt;designation&gt;.+)\.refmap" ext="tabular" />
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123 <filter>annotation['use_ref_annotation'] == 'Yes' and annotation['refmap_tmap'] != None and 'refmap' in annotation['refmap_tmap']</filter>
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124 </collection>
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125 <collection name="tmap_output" type="list" label="${tool.name} on ${on_string}: tmap">
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126 <discover_datasets pattern="gffcmp\.(?P&lt;designation&gt;.+)\.tmap" ext="tabular" />
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127 <filter>annotation['use_ref_annotation'] == 'Yes' and annotation['refmap_tmap'] != None and 'tmap' in annotation['refmap_tmap']</filter>
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128 </collection>
0
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129 </outputs>
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130 <tests>
1
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131 <test expect_num_outputs="6">
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132 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
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133 <param name="use_ref_annotation" value="Yes" />
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134 <conditional name="annotation">
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135 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />
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136 <param name="ignore_nonoverlapping_reference" value="Yes" />
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137 <param name="ignore_nonoverlapping_transfrags" value="No" />
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138 </conditional>
0
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139 <param name="use_seq_data" value="No" />
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140 <param name="discard_single_exon" value="" />
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141 <param name="max_dist_exon" value="100" />
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142 <param name="max_dist_group" value="100" />
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143 <output file="gffcompare_out1.stats" name="transcripts_stats" lines_diff="6" />
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144 <output file="gffcompare_out1.loci" name="transcripts_loci" lines_diff="2" />
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145 <output file="gffcompare_out1.tracking" name="transcripts_tracking" />
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146 <output file="gffcompare_out1.gtf" name="transcripts_combined" />
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147 <output_collection name="refmap_output" type="list" count="2">
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148 <element name="gffcompare_in1_gtf" file="gffcompare_out1-1.refmap" ftype="tabular" />
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149 <element name="gffcompare_in2_gtf" file="gffcompare_out1-2.refmap" ftype="tabular" />
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150 </output_collection>
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151 <output_collection name="tmap_output" type="list" count="2">
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152 <element name="gffcompare_in1_gtf" file="gffcompare_out1-1.tmap" ftype="tabular" />
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153 <element name="gffcompare_in2_gtf" file="gffcompare_out1-2.tmap" ftype="tabular" />
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154 </output_collection>
0
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155 </test>
1
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156 <test expect_num_outputs="4">
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157 <param ftype="gtf" name="gffinputs" value="gffcompare_in4.gtf" />
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158 <param name="use_ref_annotation" value="Yes" />
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159 <conditional name="annotation">
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160 <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" />
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161 <param name="ignore_nonoverlapping_reference" value="Yes" />
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162 <param name="ignore_nonoverlapping_transfrags" value="No" />
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163 <param name="refmap_tmap" value="" />
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164 </conditional>
0
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165 <param name="use_seq_data" value="No" />
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166 <param name="discard_single_exon" value="" />
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167 <param name="max_dist_exon" value="100" />
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168 <param name="max_dist_group" value="100" />
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169 <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" />
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170 <output file="gffcompare_out2.loci" name="transcripts_loci" />
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171 <output file="gffcompare_out2.tracking" name="transcripts_tracking" />
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172 <output file="gffcompare_out2.gtf" name="transcripts_annotated" />
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173 </test>
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174 </tests>
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175 <help>
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176 <![CDATA[
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177 **GffCompare Overview**
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178
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179 ## GffCompare
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180 * compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie).
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181 * collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples)
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182 * classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a
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183 annotation file (also in GTF/GFF3 format)
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184
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185 The original form of this program is also distributed as part of the Cufflinks suite, under the name "CuffCompare"
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186 (see manual: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/). Most of the options and parameters of CuffCompare
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187 are supported by GffCompare, while new features will likely be added to GffCompare in the future.
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188
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189 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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190 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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191 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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192 their relationship with the matching/overlapping reference transcript), but the original transcript IDs are preserved, so gffcompare can thus
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193 be used as a simple way of annotating a set of transcripts.
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194
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195 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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196 contained within other, longer isoforms. CuffCompare had the -G option to prevent collapsing of such intron redundant isoforms into
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197 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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198 and is simply ignored when given).
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199 ]]>
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200 </help>
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201 <citations>
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202 <citation type="doi">10.1038/nbt.1621</citation>
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203 </citations>
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204 </tool>