Mercurial > repos > rmarenco > hubarchivecreator
annotate hubArchiveCreator.xml @ 10:acc233161f50 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
| author | rmarenco |
|---|---|
| date | Thu, 21 Jul 2016 05:58:51 -0400 |
| parents | 1b653b332695 |
| children | d05236b15f81 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.0.2"> |
| 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
rmarenco
parents:
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changeset
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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
parents:
3
diff
changeset
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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
parents:
3
diff
changeset
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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 --> | |
| 14 <requirement type="package" version="324">ucsc-gff3togenepred</requirement> | |
| 15 <requirement type="package" version="324">ucsc-gtftogenepred</requirement> | |
| 16 <requirement type="package" version="324">ucsc-genepredtobed</requirement> | |
| 17 <requirement type="package" version="1.3.1">samtools</requirement> | |
| 18 </requirements> | |
| 19 | |
| 20 <stdio> | |
| 21 <regex match="^pass1" | |
| 22 source="stderr" | |
| 23 level="log" | |
| 24 description="bedToBigBed"/> | |
| 25 <!-- TODO: Add the case pass1 and 0 chroms --> | |
| 26 <!-- TODO: Add the case pass2 and 0 records or 0 fields --> | |
| 27 </stdio> | |
| 28 | |
| 29 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] --> | |
| 30 <command detect_errors="exit_code"><![CDATA[ | |
| 31 mkdir -p $output.extra_files_path; | |
| 32 python $__tool_directory__/hubArchiveCreator.py | |
| 33 | |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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34 ## Ask the user to enter the genome name |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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changeset
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35 --genome_name '$genome_name' |
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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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36 |
| 0 | 37 #import json |
| 38 | |
| 39 #set global data_parameter_dict = {} | |
| 40 | |
| 41 ## Function to retrieve the data of the inputs | |
| 42 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={}) | |
| 43 #set false_path = str($input_to_prepare) | |
| 44 #set name = $input_to_prepare.name | |
| 45 | |
| 46 #set data_dict = {"name": $name} | |
| 47 #silent data_dict.update($extra_data_dict) | |
| 48 | |
| 49 ## Add the ordering by taking the tool form indexes | |
| 50 #silent $data_dict.update({"order_index": $order_index + 1}) | |
| 51 | |
| 52 #silent $data_parameter_dict.update({$false_path: $data_dict}) | |
| 53 | |
| 54 #end def | |
| 55 | |
| 56 #for $i, $f in enumerate( $format ) | |
| 57 #if $f.formatChoice.format_select == "bam" | |
| 58 --bam $f.formatChoice.BAM | |
| 59 #set bam_index = $f.formatChoice.BAM.metadata.bam_index | |
| 60 #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index}) | |
| 61 #end if | |
| 62 #if $f.formatChoice.format_select == "bed" | |
| 63 #if $f.formatChoice.bedChoice.bed_select == "bed" | |
| 64 --bed $f.formatChoice.bedChoice.BED | |
| 65 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i) | |
| 66 #end if | |
| 67 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" | |
| 68 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats | |
| 69 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i) | |
| 70 #end if | |
| 71 #end if | |
| 72 #if $f.formatChoice.format_select == "bigwig" | |
| 73 --bigwig $f.formatChoice.BIGWIG | |
| 74 #silent $prepare_json($f.formatChoice.BIGWIG, $i) | |
| 75 #end if | |
| 76 #if $f.formatChoice.format_select == "gff3" | |
| 77 --gff3 $f.formatChoice.GFF3 | |
| 78 #silent $prepare_json($f.formatChoice.GFF3, $i) | |
| 79 #end if | |
| 80 #if $f.formatChoice.format_select == "gtf" | |
| 81 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 | |
| 82 --gtf $f.formatChoice.GTF | |
| 83 #silent $prepare_json($f.formatChoice.GTF, $i) | |
| 84 #end if | |
| 85 #end for | |
| 86 | |
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10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
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87 ## We combine the fasta file dataset name with his false path in a JSON object |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
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88 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name}) |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
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89 -f '$fasta_json' |
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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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90 |
| 0 | 91 ## Dump the final json |
| 92 #set all_data_json = json.dumps($data_parameter_dict) | |
| 93 | |
| 94 --data_json '$all_data_json' | |
| 95 | |
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10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
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96 ## Retrieve the user email |
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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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97 --user_email $__user_email__ |
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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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98 |
| 0 | 99 -d $__tool_directory__ -e $output.files_path -o $output; |
| 100 ]]></command> | |
| 101 | |
| 102 <inputs> | |
| 103 <param | |
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10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
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104 name="genome_name" |
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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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105 type="text" |
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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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106 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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diff
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107 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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diff
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108 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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changeset
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109 /> |
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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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110 <param |
| 0 | 111 format="fasta" |
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10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
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112 name="fasta_file" |
| 0 | 113 type="data" |
| 114 label="Reference genome" | |
| 115 /> | |
| 116 <repeat name="format" title="Formats"> | |
| 117 <conditional name="formatChoice"> | |
| 118 <param name="format_select" type="select" label="Format"> | |
| 119 <option value="bam" selected="true">BAM</option> | |
| 120 <option value="bed">BED</option> | |
| 121 <option value="bigwig">BIGWIG</option> | |
| 122 <option value="gff3">GFF3</option> | |
| 123 <option value="gtf">GTF</option> | |
| 124 </param> | |
| 125 | |
| 126 <when value="bam"> | |
| 127 <param | |
| 128 format="bam" | |
| 129 name="BAM" | |
| 130 type="data" | |
| 131 label="BAM File" | |
| 132 /> | |
| 133 </when> | |
| 134 <when value="bigwig"> | |
| 135 <param | |
| 136 format="bigwig" | |
| 137 name="BIGWIG" | |
| 138 type="data" | |
| 139 label="BIGWIG File" | |
| 140 /> | |
| 141 </when> | |
| 142 <when value="gff3"> | |
| 143 <param | |
| 144 format="gff3" | |
| 145 name="GFF3" | |
| 146 type="data" | |
| 147 label="GFF3 File" | |
| 148 /> | |
| 149 </when> | |
| 150 <when value="gtf"> | |
| 151 <param | |
| 152 format="gtf" | |
| 153 name="GTF" | |
| 154 type="data" | |
| 155 label="GTF File" | |
| 156 /> | |
| 157 </when> | |
| 158 <when value="bed"> | |
| 159 <conditional name="bedChoice"> | |
| 160 <param name="bed_select" type="select" label="Bed Choice"> | |
| 161 <option value="bed" selected="true">Generic BED</option> | |
| 162 <option value="bed_simple_repeats_option">BED simple repeats</option> | |
| 163 </param> | |
| 164 <when value="bed"> | |
| 165 <param | |
| 166 format="bed" | |
| 167 name="BED" | |
| 168 type="data" | |
| 169 label="Generic Bed File Choice" | |
| 170 /> | |
| 171 </when> | |
| 172 <when value="bed_simple_repeats_option"> | |
| 173 <param | |
| 174 format="bed" | |
| 175 name="BED_simple_repeats" | |
| 176 type="data" | |
| 177 label="Bed Simple Repeats (Bed4+12) File" | |
| 178 /> | |
| 179 </when> | |
| 180 </conditional> | |
| 181 </when> | |
| 182 </conditional> | |
| 183 </repeat> | |
| 184 </inputs> | |
| 185 | |
| 186 <outputs> | |
| 187 <data format="trackhub" name="output"/> | |
| 188 </outputs> | |
| 189 | |
| 190 <tests> | |
| 191 <!-- Can also use assert_command to test command --> | |
| 192 <!-- Testing GFF3 input --> | |
| 193 <test> | |
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10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
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194 <param name="fasta_file" value="dbia3.fa"/> |
| 0 | 195 <repeat name="format"> |
| 196 <conditional name="formatChoice"> | |
| 197 <param name="format_select" value="gff3"/> | |
| 198 <param name="GFF3" value="augustusDbia3.gff3"/> | |
| 199 </conditional> | |
| 200 </repeat> | |
| 201 <repeat name="format"> | |
| 202 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> | |
| 203 <!-- TODO: Ask why the tests are not passing with this xml: | |
| 204 Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history' | |
| 205 <conditional name="formatChoice"> | |
| 206 <param name="format_select" value="bed"/> | |
| 207 <conditional name="bedChoice"> | |
| 208 <param name="bed_select" value="bed_simple_repeats_option"/> | |
| 209 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> | |
| 210 </conditional> | |
| 211 </conditional> | |
| 212 --> | |
| 213 </repeat> | |
| 214 | |
| 215 <output name="output"> | |
| 216 <assert_contents> | |
| 217 <has_text text="myHub"/> | |
| 218 </assert_contents> | |
| 219 <assert_contents> | |
| 220 <has_text text="dbia3_trfBig.bb"/> | |
| 221 </assert_contents> | |
| 222 <assert_contents> | |
| 223 <has_text text="SAODOAii qwwqod92921"/> | |
| 224 </assert_contents> | |
| 225 </output> | |
| 226 </test> | |
| 227 <test> | |
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10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
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228 <param name="fasta_file" value="dbia3.fa"/> |
| 0 | 229 <param name="GFF3" value="augustusDbia3.gff3"/> |
| 230 <output name="output" file="augustusOutput.html" lines_diff="2"> | |
| 231 <extra_files type="directory" value="myHub"/> | |
| 232 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/> | |
| 233 </output> | |
| 234 </test> | |
| 235 <!-- Testing Generic BED input --> | |
| 236 <!-- Testing Bed Simple repeat input --> | |
| 237 </tests> | |
| 238 | |
| 239 <help> | |
| 240 This Galaxy tool permits to prepare your files to be ready for | |
| 241 Assembly Hub visualization. | |
| 242 </help> | |
| 243 </tool> |