Mercurial > repos > rmarenco > hubarchivecreator
annotate hubArchiveCreator.xml @ 14:cbd8982c9f51 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 38f01a73fea83321618501978a3a505b5e8ab527
| author | rmarenco |
|---|---|
| date | Mon, 15 Aug 2016 19:19:32 -0400 |
| parents | 25809f699cb3 |
| children | 2a45cd656e8e |
| 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
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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
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11 <requirement type="package" version="0.0.1">genePredToBed</requirement> |
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cbd8982c9f51
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 38f01a73fea83321618501978a3a505b5e8ab527
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12 <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement> |
| 0 | 13 <requirement type="package" version="1.2">samtools</requirement> |
| 14 <!-- Conda dependencies --> | |
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d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
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15 <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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16 <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
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17 <requirement type="package" version="324">ucsc-genepredtobed</requirement> |
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25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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18 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement> |
| 0 | 19 <requirement type="package" version="324">ucsc-gff3togenepred</requirement> |
| 20 <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
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21 <requirement type="package" version="324">ucsc-twobitinfo</requirement> |
| 0 | 22 <requirement type="package" version="1.3.1">samtools</requirement> |
| 23 </requirements> | |
| 24 | |
| 25 <stdio> | |
| 26 <regex match="^pass1" | |
| 27 source="stderr" | |
| 28 level="log" | |
| 29 description="bedToBigBed"/> | |
| 30 <!-- TODO: Add the case pass1 and 0 chroms --> | |
| 31 <!-- TODO: Add the case pass2 and 0 records or 0 fields --> | |
| 32 </stdio> | |
| 33 | |
| 34 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] --> | |
| 35 <command detect_errors="exit_code"><![CDATA[ | |
| 36 mkdir -p $output.extra_files_path; | |
| 37 python $__tool_directory__/hubArchiveCreator.py | |
| 38 | |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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39 ## Ask the user to enter the genome name |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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40 --genome_name '$genome_name' |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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41 |
| 0 | 42 #import json |
| 43 | |
| 44 #set global data_parameter_dict = {} | |
| 45 | |
| 46 ## Function to retrieve the data of the inputs | |
| 47 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={}) | |
| 48 #set false_path = str($input_to_prepare) | |
| 49 #set name = $input_to_prepare.name | |
| 50 | |
| 51 #set data_dict = {"name": $name} | |
| 52 #silent data_dict.update($extra_data_dict) | |
| 53 | |
| 54 ## Add the ordering by taking the tool form indexes | |
| 55 #silent $data_dict.update({"order_index": $order_index + 1}) | |
| 56 | |
| 57 #silent $data_parameter_dict.update({$false_path: $data_dict}) | |
| 58 | |
| 59 #end def | |
| 60 | |
| 61 #for $i, $f in enumerate( $format ) | |
| 62 #if $f.formatChoice.format_select == "bam" | |
| 63 --bam $f.formatChoice.BAM | |
| 64 #set bam_index = $f.formatChoice.BAM.metadata.bam_index | |
| 65 #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index}) | |
| 66 #end if | |
| 67 #if $f.formatChoice.format_select == "bed" | |
| 68 #if $f.formatChoice.bedChoice.bed_select == "bed" | |
| 69 --bed $f.formatChoice.bedChoice.BED | |
| 70 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i) | |
| 71 #end if | |
| 72 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" | |
| 73 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats | |
| 74 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i) | |
| 75 #end if | |
| 76 #end if | |
| 77 #if $f.formatChoice.format_select == "bigwig" | |
| 78 --bigwig $f.formatChoice.BIGWIG | |
| 79 #silent $prepare_json($f.formatChoice.BIGWIG, $i) | |
| 80 #end if | |
| 81 #if $f.formatChoice.format_select == "gff3" | |
| 82 --gff3 $f.formatChoice.GFF3 | |
| 83 #silent $prepare_json($f.formatChoice.GFF3, $i) | |
| 84 #end if | |
| 85 #if $f.formatChoice.format_select == "gtf" | |
| 86 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 | |
| 87 --gtf $f.formatChoice.GTF | |
| 88 #silent $prepare_json($f.formatChoice.GTF, $i) | |
| 89 #end if | |
| 90 #end for | |
| 91 | |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
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92 ## We combine the fasta file dataset name with his false path in a JSON object |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
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93 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name}) |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
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94 -f '$fasta_json' |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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95 |
| 0 | 96 ## Dump the final json |
| 97 #set all_data_json = json.dumps($data_parameter_dict) | |
| 98 | |
| 99 --data_json '$all_data_json' | |
| 100 | |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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101 ## Retrieve the user email |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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102 --user_email $__user_email__ |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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103 |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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104 -d $__tool_directory__ |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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105 |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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106 -e $output.files_path |
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25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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107 |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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108 $advanced_options.debug_mode |
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25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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109 |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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110 -o $output; |
| 0 | 111 ]]></command> |
| 112 | |
| 113 <inputs> | |
| 114 <param | |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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115 name="genome_name" |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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116 type="text" |
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117 size="30" |
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118 value="unknown" |
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119 label="UCSC Genome Browser assembly ID" |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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120 /> |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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121 <param |
| 0 | 122 format="fasta" |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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123 name="fasta_file" |
| 0 | 124 type="data" |
| 125 label="Reference genome" | |
| 126 /> | |
| 127 <repeat name="format" title="Formats"> | |
| 128 <conditional name="formatChoice"> | |
| 129 <param name="format_select" type="select" label="Format"> | |
| 130 <option value="bam" selected="true">BAM</option> | |
| 131 <option value="bed">BED</option> | |
| 132 <option value="bigwig">BIGWIG</option> | |
| 133 <option value="gff3">GFF3</option> | |
| 134 <option value="gtf">GTF</option> | |
| 135 </param> | |
| 136 | |
| 137 <when value="bam"> | |
| 138 <param | |
| 139 format="bam" | |
| 140 name="BAM" | |
| 141 type="data" | |
| 142 label="BAM File" | |
| 143 /> | |
| 144 </when> | |
| 145 <when value="bigwig"> | |
| 146 <param | |
| 147 format="bigwig" | |
| 148 name="BIGWIG" | |
| 149 type="data" | |
| 150 label="BIGWIG File" | |
| 151 /> | |
| 152 </when> | |
| 153 <when value="gff3"> | |
| 154 <param | |
| 155 format="gff3" | |
| 156 name="GFF3" | |
| 157 type="data" | |
| 158 label="GFF3 File" | |
| 159 /> | |
| 160 </when> | |
| 161 <when value="gtf"> | |
| 162 <param | |
| 163 format="gtf" | |
| 164 name="GTF" | |
| 165 type="data" | |
| 166 label="GTF File" | |
| 167 /> | |
| 168 </when> | |
| 169 <when value="bed"> | |
| 170 <conditional name="bedChoice"> | |
| 171 <param name="bed_select" type="select" label="Bed Choice"> | |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
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172 <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
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173 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> |
| 0 | 174 </param> |
| 175 <when value="bed"> | |
| 176 <param | |
| 177 format="bed" | |
| 178 name="BED" | |
| 179 type="data" | |
| 180 label="Generic Bed File Choice" | |
| 181 /> | |
| 182 </when> | |
| 183 <when value="bed_simple_repeats_option"> | |
| 184 <param | |
| 185 format="bed" | |
| 186 name="BED_simple_repeats" | |
| 187 type="data" | |
| 188 label="Bed Simple Repeats (Bed4+12) File" | |
| 189 /> | |
| 190 </when> | |
| 191 </conditional> | |
| 192 </when> | |
| 193 </conditional> | |
| 194 </repeat> | |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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195 <conditional name="advanced_options"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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196 <param name="advanced_options_selector" type="select" label="Advanced options"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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197 <option value="off" selected="true">Hide advanced options</option> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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198 <option value="on">Display advanced options</option> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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199 </param> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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200 <!-- TODO: Avoid redundancy here --> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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201 <when value="on"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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202 <param name="debug_mode" type="boolean" |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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203 label="Activate debug mode" checked="false" |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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204 truevalue="--debug_mode" falsevalue=""> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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205 <help> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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206 Use this option if you are a G-OnRamp developer |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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207 </help> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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208 </param> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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209 </when> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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210 <when value="off"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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211 <param name="debug_mode" type="hidden" |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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212 value=""> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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213 </param> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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214 </when> |
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25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
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215 </conditional> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
216 </inputs> |
| 0 | 217 |
| 218 <outputs> | |
| 219 <data format="trackhub" name="output"/> | |
| 220 </outputs> | |
| 221 | |
| 222 <tests> | |
| 223 <!-- Can also use assert_command to test command --> | |
| 224 <!-- Testing GFF3 input --> | |
| 225 <test> | |
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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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226 <param name="fasta_file" value="dbia3.fa"/> |
| 0 | 227 <repeat name="format"> |
| 228 <conditional name="formatChoice"> | |
| 229 <param name="format_select" value="gff3"/> | |
| 230 <param name="GFF3" value="augustusDbia3.gff3"/> | |
| 231 </conditional> | |
| 232 </repeat> | |
| 233 <repeat name="format"> | |
| 234 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> | |
| 235 <!-- TODO: Ask why the tests are not passing with this xml: | |
| 236 Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history' | |
| 237 <conditional name="formatChoice"> | |
| 238 <param name="format_select" value="bed"/> | |
| 239 <conditional name="bedChoice"> | |
| 240 <param name="bed_select" value="bed_simple_repeats_option"/> | |
| 241 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> | |
| 242 </conditional> | |
| 243 </conditional> | |
| 244 --> | |
| 245 </repeat> | |
| 246 | |
| 247 <output name="output"> | |
| 248 <assert_contents> | |
| 249 <has_text text="myHub"/> | |
| 250 </assert_contents> | |
| 251 <assert_contents> | |
| 252 <has_text text="dbia3_trfBig.bb"/> | |
| 253 </assert_contents> | |
| 254 <assert_contents> | |
| 255 <has_text text="SAODOAii qwwqod92921"/> | |
| 256 </assert_contents> | |
| 257 </output> | |
| 258 </test> | |
| 259 <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
|
260 <param name="fasta_file" value="dbia3.fa"/> |
| 0 | 261 <param name="GFF3" value="augustusDbia3.gff3"/> |
| 262 <output name="output" file="augustusOutput.html" lines_diff="2"> | |
| 263 <extra_files type="directory" value="myHub"/> | |
| 264 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/> | |
| 265 </output> | |
| 266 </test> | |
| 267 <!-- Testing Generic BED input --> | |
| 268 <!-- Testing Bed Simple repeat input --> | |
| 269 </tests> | |
| 270 | |
| 271 <help> | |
| 272 This Galaxy tool permits to prepare your files to be ready for | |
| 273 Assembly Hub visualization. | |
| 274 </help> | |
| 275 </tool> |