Mercurial > repos > rmarenco > hubarchivecreator
annotate hubArchiveCreator.xml @ 12:747475757cb0 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 85389def8ed35b3dc08701963dcae4afd1b5b50a
| author | rmarenco |
|---|---|
| date | Wed, 27 Jul 2016 10:43:58 -0400 |
| parents | d05236b15f81 |
| children | 25809f699cb3 |
| rev | line source |
|---|---|
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d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
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1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0"> |
| 0 | 2 <description> |
| 3 This Galaxy tool permits to prepare your files to be ready for | |
| 4 Assembly Hub visualization. | |
| 5 </description> | |
| 6 | |
| 7 <requirements> | |
| 8 <requirement type="package" version="312">ucsc_tools</requirement> | |
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1b653b332695
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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9 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement> |
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1b653b332695
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
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10 <requirement type="package" version="0.0.1">gtfToGenePred</requirement> |
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1b653b332695
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
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11 <requirement type="package" version="0.0.1">genePredToBed</requirement> |
| 0 | 12 <requirement type="package" version="1.2">samtools</requirement> |
| 13 <!-- Conda dependencies --> | |
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d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
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14 <requirement type="package" version="332">ucsc-bedtobigbed</requirement> |
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d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
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15 <requirement type="package" version="332">ucsc-fatotwobit</requirement> |
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d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
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16 <requirement type="package" version="324">ucsc-genepredtobed</requirement> |
| 0 | 17 <requirement type="package" version="324">ucsc-gff3togenepred</requirement> |
| 18 <requirement type="package" version="324">ucsc-gtftogenepred</requirement> | |
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d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
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19 <requirement type="package" version="324">ucsc-twobitinfo</requirement> |
| 0 | 20 <requirement type="package" version="1.3.1">samtools</requirement> |
| 21 </requirements> | |
| 22 | |
| 23 <stdio> | |
| 24 <regex match="^pass1" | |
| 25 source="stderr" | |
| 26 level="log" | |
| 27 description="bedToBigBed"/> | |
| 28 <!-- TODO: Add the case pass1 and 0 chroms --> | |
| 29 <!-- TODO: Add the case pass2 and 0 records or 0 fields --> | |
| 30 </stdio> | |
| 31 | |
| 32 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] --> | |
| 33 <command detect_errors="exit_code"><![CDATA[ | |
| 34 mkdir -p $output.extra_files_path; | |
| 35 python $__tool_directory__/hubArchiveCreator.py | |
| 36 | |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
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37 ## Ask the user to enter the genome name |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
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38 --genome_name '$genome_name' |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
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39 |
| 0 | 40 #import json |
| 41 | |
| 42 #set global data_parameter_dict = {} | |
| 43 | |
| 44 ## Function to retrieve the data of the inputs | |
| 45 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={}) | |
| 46 #set false_path = str($input_to_prepare) | |
| 47 #set name = $input_to_prepare.name | |
| 48 | |
| 49 #set data_dict = {"name": $name} | |
| 50 #silent data_dict.update($extra_data_dict) | |
| 51 | |
| 52 ## Add the ordering by taking the tool form indexes | |
| 53 #silent $data_dict.update({"order_index": $order_index + 1}) | |
| 54 | |
| 55 #silent $data_parameter_dict.update({$false_path: $data_dict}) | |
| 56 | |
| 57 #end def | |
| 58 | |
| 59 #for $i, $f in enumerate( $format ) | |
| 60 #if $f.formatChoice.format_select == "bam" | |
| 61 --bam $f.formatChoice.BAM | |
| 62 #set bam_index = $f.formatChoice.BAM.metadata.bam_index | |
| 63 #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index}) | |
| 64 #end if | |
| 65 #if $f.formatChoice.format_select == "bed" | |
| 66 #if $f.formatChoice.bedChoice.bed_select == "bed" | |
| 67 --bed $f.formatChoice.bedChoice.BED | |
| 68 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i) | |
| 69 #end if | |
| 70 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" | |
| 71 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats | |
| 72 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i) | |
| 73 #end if | |
| 74 #end if | |
| 75 #if $f.formatChoice.format_select == "bigwig" | |
| 76 --bigwig $f.formatChoice.BIGWIG | |
| 77 #silent $prepare_json($f.formatChoice.BIGWIG, $i) | |
| 78 #end if | |
| 79 #if $f.formatChoice.format_select == "gff3" | |
| 80 --gff3 $f.formatChoice.GFF3 | |
| 81 #silent $prepare_json($f.formatChoice.GFF3, $i) | |
| 82 #end if | |
| 83 #if $f.formatChoice.format_select == "gtf" | |
| 84 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 | |
| 85 --gtf $f.formatChoice.GTF | |
| 86 #silent $prepare_json($f.formatChoice.GTF, $i) | |
| 87 #end if | |
| 88 #end for | |
| 89 | |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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diff
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90 ## We combine the fasta file dataset name with his false path in a JSON object |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
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91 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name}) |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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diff
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92 -f '$fasta_json' |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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diff
changeset
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93 |
| 0 | 94 ## Dump the final json |
| 95 #set all_data_json = json.dumps($data_parameter_dict) | |
| 96 | |
| 97 --data_json '$all_data_json' | |
| 98 | |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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99 ## Retrieve the user email |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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100 --user_email $__user_email__ |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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101 |
| 0 | 102 -d $__tool_directory__ -e $output.files_path -o $output; |
| 103 ]]></command> | |
| 104 | |
| 105 <inputs> | |
| 106 <param | |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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107 name="genome_name" |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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108 type="text" |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
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109 size="30" |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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110 value="unknown" |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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111 label="UCSC Genome Browser assembly ID" |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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112 /> |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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113 <param |
| 0 | 114 format="fasta" |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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115 name="fasta_file" |
| 0 | 116 type="data" |
| 117 label="Reference genome" | |
| 118 /> | |
| 119 <repeat name="format" title="Formats"> | |
| 120 <conditional name="formatChoice"> | |
| 121 <param name="format_select" type="select" label="Format"> | |
| 122 <option value="bam" selected="true">BAM</option> | |
| 123 <option value="bed">BED</option> | |
| 124 <option value="bigwig">BIGWIG</option> | |
| 125 <option value="gff3">GFF3</option> | |
| 126 <option value="gtf">GTF</option> | |
| 127 </param> | |
| 128 | |
| 129 <when value="bam"> | |
| 130 <param | |
| 131 format="bam" | |
| 132 name="BAM" | |
| 133 type="data" | |
| 134 label="BAM File" | |
| 135 /> | |
| 136 </when> | |
| 137 <when value="bigwig"> | |
| 138 <param | |
| 139 format="bigwig" | |
| 140 name="BIGWIG" | |
| 141 type="data" | |
| 142 label="BIGWIG File" | |
| 143 /> | |
| 144 </when> | |
| 145 <when value="gff3"> | |
| 146 <param | |
| 147 format="gff3" | |
| 148 name="GFF3" | |
| 149 type="data" | |
| 150 label="GFF3 File" | |
| 151 /> | |
| 152 </when> | |
| 153 <when value="gtf"> | |
| 154 <param | |
| 155 format="gtf" | |
| 156 name="GTF" | |
| 157 type="data" | |
| 158 label="GTF File" | |
| 159 /> | |
| 160 </when> | |
| 161 <when value="bed"> | |
| 162 <conditional name="bedChoice"> | |
| 163 <param name="bed_select" type="select" label="Bed Choice"> | |
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d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
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diff
changeset
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164 <option value="bed" selected="true">BED Generic (bed3+)</option> |
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d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
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diff
changeset
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165 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> |
| 0 | 166 </param> |
| 167 <when value="bed"> | |
| 168 <param | |
| 169 format="bed" | |
| 170 name="BED" | |
| 171 type="data" | |
| 172 label="Generic Bed File Choice" | |
| 173 /> | |
| 174 </when> | |
| 175 <when value="bed_simple_repeats_option"> | |
| 176 <param | |
| 177 format="bed" | |
| 178 name="BED_simple_repeats" | |
| 179 type="data" | |
| 180 label="Bed Simple Repeats (Bed4+12) File" | |
| 181 /> | |
| 182 </when> | |
| 183 </conditional> | |
| 184 </when> | |
| 185 </conditional> | |
| 186 </repeat> | |
| 187 </inputs> | |
| 188 | |
| 189 <outputs> | |
| 190 <data format="trackhub" name="output"/> | |
| 191 </outputs> | |
| 192 | |
| 193 <tests> | |
| 194 <!-- Can also use assert_command to test command --> | |
| 195 <!-- Testing GFF3 input --> | |
| 196 <test> | |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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197 <param name="fasta_file" value="dbia3.fa"/> |
| 0 | 198 <repeat name="format"> |
| 199 <conditional name="formatChoice"> | |
| 200 <param name="format_select" value="gff3"/> | |
| 201 <param name="GFF3" value="augustusDbia3.gff3"/> | |
| 202 </conditional> | |
| 203 </repeat> | |
| 204 <repeat name="format"> | |
| 205 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> | |
| 206 <!-- TODO: Ask why the tests are not passing with this xml: | |
| 207 Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history' | |
| 208 <conditional name="formatChoice"> | |
| 209 <param name="format_select" value="bed"/> | |
| 210 <conditional name="bedChoice"> | |
| 211 <param name="bed_select" value="bed_simple_repeats_option"/> | |
| 212 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> | |
| 213 </conditional> | |
| 214 </conditional> | |
| 215 --> | |
| 216 </repeat> | |
| 217 | |
| 218 <output name="output"> | |
| 219 <assert_contents> | |
| 220 <has_text text="myHub"/> | |
| 221 </assert_contents> | |
| 222 <assert_contents> | |
| 223 <has_text text="dbia3_trfBig.bb"/> | |
| 224 </assert_contents> | |
| 225 <assert_contents> | |
| 226 <has_text text="SAODOAii qwwqod92921"/> | |
| 227 </assert_contents> | |
| 228 </output> | |
| 229 </test> | |
| 230 <test> | |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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231 <param name="fasta_file" value="dbia3.fa"/> |
| 0 | 232 <param name="GFF3" value="augustusDbia3.gff3"/> |
| 233 <output name="output" file="augustusOutput.html" lines_diff="2"> | |
| 234 <extra_files type="directory" value="myHub"/> | |
| 235 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/> | |
| 236 </output> | |
| 237 </test> | |
| 238 <!-- Testing Generic BED input --> | |
| 239 <!-- Testing Bed Simple repeat input --> | |
| 240 </tests> | |
| 241 | |
| 242 <help> | |
| 243 This Galaxy tool permits to prepare your files to be ready for | |
| 244 Assembly Hub visualization. | |
| 245 </help> | |
| 246 </tool> |