Mercurial > repos > rmarenco > hubarchivecreator
annotate hubArchiveCreator.xml @ 15:2a45cd656e8e draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit f11032a9df62c79a46f6e4a055a3c7ae981ea721
| author | rmarenco |
|---|---|
| date | Fri, 02 Sep 2016 15:41:51 -0400 |
| parents | cbd8982c9f51 |
| children | 3233451a3bd6 |
| 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> | |
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2a45cd656e8e
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit f11032a9df62c79a46f6e4a055a3c7ae981ea721
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8 <!-- Conda dependencies --> |
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2a45cd656e8e
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit f11032a9df62c79a46f6e4a055a3c7ae981ea721
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9 <requirement type="package" version="332">ucsc-bedtobigbed</requirement> |
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2a45cd656e8e
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit f11032a9df62c79a46f6e4a055a3c7ae981ea721
rmarenco
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10 <requirement type="package" version="332">ucsc-fatotwobit</requirement> |
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2a45cd656e8e
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit f11032a9df62c79a46f6e4a055a3c7ae981ea721
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11 <requirement type="package" version="332">ucsc-genepredtobed</requirement> |
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2a45cd656e8e
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit f11032a9df62c79a46f6e4a055a3c7ae981ea721
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12 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement> |
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2a45cd656e8e
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit f11032a9df62c79a46f6e4a055a3c7ae981ea721
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13 <requirement type="package" version="332">ucsc-gff3togenepred</requirement> |
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2a45cd656e8e
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit f11032a9df62c79a46f6e4a055a3c7ae981ea721
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14 <requirement type="package" version="332">ucsc-gtftogenepred</requirement> |
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2a45cd656e8e
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit f11032a9df62c79a46f6e4a055a3c7ae981ea721
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15 <requirement type="package" version="332">ucsc-twobitinfo</requirement> |
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2a45cd656e8e
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit f11032a9df62c79a46f6e4a055a3c7ae981ea721
rmarenco
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16 <requirement type="package" version="1.3">samtools</requirement> |
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2a45cd656e8e
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit f11032a9df62c79a46f6e4a055a3c7ae981ea721
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17 <!-- ToolShed dependencies --> |
| 0 | 18 <requirement type="package" version="312">ucsc_tools</requirement> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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19 <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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20 <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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21 <requirement type="package" version="0.0.1">genePredToBed</requirement> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 38f01a73fea83321618501978a3a505b5e8ab527
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22 <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement> |
| 0 | 23 <requirement type="package" version="1.2">samtools</requirement> |
| 24 </requirements> | |
| 25 | |
| 26 <stdio> | |
| 27 <regex match="^pass1" | |
| 28 source="stderr" | |
| 29 level="log" | |
| 30 description="bedToBigBed"/> | |
| 31 <!-- TODO: Add the case pass1 and 0 chroms --> | |
| 32 <!-- TODO: Add the case pass2 and 0 records or 0 fields --> | |
| 33 </stdio> | |
| 34 | |
| 35 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] --> | |
| 36 <command detect_errors="exit_code"><![CDATA[ | |
| 37 mkdir -p $output.extra_files_path; | |
| 38 python $__tool_directory__/hubArchiveCreator.py | |
| 39 | |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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40 ## Ask the user to enter the genome name |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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41 --genome_name '$genome_name' |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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42 |
| 0 | 43 #import json |
| 44 | |
| 45 #set global data_parameter_dict = {} | |
| 46 | |
| 47 ## Function to retrieve the data of the inputs | |
| 48 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={}) | |
| 49 #set false_path = str($input_to_prepare) | |
| 50 #set name = $input_to_prepare.name | |
| 51 | |
| 52 #set data_dict = {"name": $name} | |
| 53 #silent data_dict.update($extra_data_dict) | |
| 54 | |
| 55 ## Add the ordering by taking the tool form indexes | |
| 56 #silent $data_dict.update({"order_index": $order_index + 1}) | |
| 57 | |
| 58 #silent $data_parameter_dict.update({$false_path: $data_dict}) | |
| 59 | |
| 60 #end def | |
| 61 | |
| 62 #for $i, $f in enumerate( $format ) | |
| 63 #if $f.formatChoice.format_select == "bam" | |
| 64 --bam $f.formatChoice.BAM | |
| 65 #set bam_index = $f.formatChoice.BAM.metadata.bam_index | |
| 66 #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index}) | |
| 67 #end if | |
| 68 #if $f.formatChoice.format_select == "bed" | |
| 69 #if $f.formatChoice.bedChoice.bed_select == "bed" | |
| 70 --bed $f.formatChoice.bedChoice.BED | |
| 71 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i) | |
| 72 #end if | |
| 73 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" | |
| 74 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats | |
| 75 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i) | |
| 76 #end if | |
| 77 #end if | |
| 78 #if $f.formatChoice.format_select == "bigwig" | |
| 79 --bigwig $f.formatChoice.BIGWIG | |
| 80 #silent $prepare_json($f.formatChoice.BIGWIG, $i) | |
| 81 #end if | |
| 82 #if $f.formatChoice.format_select == "gff3" | |
| 83 --gff3 $f.formatChoice.GFF3 | |
| 84 #silent $prepare_json($f.formatChoice.GFF3, $i) | |
| 85 #end if | |
| 86 #if $f.formatChoice.format_select == "gtf" | |
| 87 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 | |
| 88 --gtf $f.formatChoice.GTF | |
| 89 #silent $prepare_json($f.formatChoice.GTF, $i) | |
| 90 #end if | |
| 91 #end for | |
| 92 | |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
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93 ## We combine the fasta file dataset name with his false path in a JSON object |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
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94 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name}) |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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95 -f '$fasta_json' |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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96 |
| 0 | 97 ## Dump the final json |
| 98 #set all_data_json = json.dumps($data_parameter_dict) | |
| 99 | |
| 100 --data_json '$all_data_json' | |
| 101 | |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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102 ## 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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103 --user_email $__user_email__ |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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104 |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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105 -d $__tool_directory__ |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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106 |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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107 -e $output.files_path |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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108 |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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109 $advanced_options.debug_mode |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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110 |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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111 -o $output; |
| 0 | 112 ]]></command> |
| 113 | |
| 114 <inputs> | |
| 115 <param | |
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116 name="genome_name" |
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117 type="text" |
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118 size="30" |
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119 value="unknown" |
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120 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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121 /> |
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acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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122 <param |
| 0 | 123 format="fasta" |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
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124 name="fasta_file" |
| 0 | 125 type="data" |
| 126 label="Reference genome" | |
| 127 /> | |
| 128 <repeat name="format" title="Formats"> | |
| 129 <conditional name="formatChoice"> | |
| 130 <param name="format_select" type="select" label="Format"> | |
| 131 <option value="bam" selected="true">BAM</option> | |
| 132 <option value="bed">BED</option> | |
| 133 <option value="bigwig">BIGWIG</option> | |
| 134 <option value="gff3">GFF3</option> | |
| 135 <option value="gtf">GTF</option> | |
| 136 </param> | |
| 137 | |
| 138 <when value="bam"> | |
| 139 <param | |
| 140 format="bam" | |
| 141 name="BAM" | |
| 142 type="data" | |
| 143 label="BAM File" | |
| 144 /> | |
| 145 </when> | |
| 146 <when value="bigwig"> | |
| 147 <param | |
| 148 format="bigwig" | |
| 149 name="BIGWIG" | |
| 150 type="data" | |
| 151 label="BIGWIG File" | |
| 152 /> | |
| 153 </when> | |
| 154 <when value="gff3"> | |
| 155 <param | |
| 156 format="gff3" | |
| 157 name="GFF3" | |
| 158 type="data" | |
| 159 label="GFF3 File" | |
| 160 /> | |
| 161 </when> | |
| 162 <when value="gtf"> | |
| 163 <param | |
| 164 format="gtf" | |
| 165 name="GTF" | |
| 166 type="data" | |
| 167 label="GTF File" | |
| 168 /> | |
| 169 </when> | |
| 170 <when value="bed"> | |
| 171 <conditional name="bedChoice"> | |
| 172 <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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173 <option value="bed" selected="true">BED Generic (bed3+)</option> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
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174 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> |
| 0 | 175 </param> |
| 176 <when value="bed"> | |
| 177 <param | |
| 178 format="bed" | |
| 179 name="BED" | |
| 180 type="data" | |
| 181 label="Generic Bed File Choice" | |
| 182 /> | |
| 183 </when> | |
| 184 <when value="bed_simple_repeats_option"> | |
| 185 <param | |
| 186 format="bed" | |
| 187 name="BED_simple_repeats" | |
| 188 type="data" | |
| 189 label="Bed Simple Repeats (Bed4+12) File" | |
| 190 /> | |
| 191 </when> | |
| 192 </conditional> | |
| 193 </when> | |
| 194 </conditional> | |
| 195 </repeat> | |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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196 <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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197 <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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198 <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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199 <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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200 </param> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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201 <!-- 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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202 <when value="on"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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203 <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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204 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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205 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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206 <help> |
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207 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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208 </help> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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209 </param> |
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210 </when> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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211 <when value="off"> |
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212 <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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213 value=""> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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214 </param> |
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215 </when> |
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216 </conditional> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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217 </inputs> |
| 0 | 218 |
| 219 <outputs> | |
| 220 <data format="trackhub" name="output"/> | |
| 221 </outputs> | |
| 222 | |
| 223 <tests> | |
| 224 <!-- Can also use assert_command to test command --> | |
| 225 <!-- Testing GFF3 input --> | |
| 226 <test> | |
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227 <param name="fasta_file" value="dbia3.fa"/> |
| 0 | 228 <repeat name="format"> |
| 229 <conditional name="formatChoice"> | |
| 230 <param name="format_select" value="gff3"/> | |
| 231 <param name="GFF3" value="augustusDbia3.gff3"/> | |
| 232 </conditional> | |
| 233 </repeat> | |
| 234 <repeat name="format"> | |
| 235 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> | |
| 236 <!-- TODO: Ask why the tests are not passing with this xml: | |
| 237 Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history' | |
| 238 <conditional name="formatChoice"> | |
| 239 <param name="format_select" value="bed"/> | |
| 240 <conditional name="bedChoice"> | |
| 241 <param name="bed_select" value="bed_simple_repeats_option"/> | |
| 242 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> | |
| 243 </conditional> | |
| 244 </conditional> | |
| 245 --> | |
| 246 </repeat> | |
| 247 | |
| 248 <output name="output"> | |
| 249 <assert_contents> | |
| 250 <has_text text="myHub"/> | |
| 251 </assert_contents> | |
| 252 <assert_contents> | |
| 253 <has_text text="dbia3_trfBig.bb"/> | |
| 254 </assert_contents> | |
| 255 <assert_contents> | |
| 256 <has_text text="SAODOAii qwwqod92921"/> | |
| 257 </assert_contents> | |
| 258 </output> | |
| 259 </test> | |
| 260 <test> | |
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261 <param name="fasta_file" value="dbia3.fa"/> |
| 0 | 262 <param name="GFF3" value="augustusDbia3.gff3"/> |
| 263 <output name="output" file="augustusOutput.html" lines_diff="2"> | |
| 264 <extra_files type="directory" value="myHub"/> | |
| 265 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/> | |
| 266 </output> | |
| 267 </test> | |
| 268 <!-- Testing Generic BED input --> | |
| 269 <!-- Testing Bed Simple repeat input --> | |
| 270 </tests> | |
| 271 | |
| 272 <help> | |
| 273 This Galaxy tool permits to prepare your files to be ready for | |
| 274 Assembly Hub visualization. | |
| 275 </help> | |
| 276 </tool> |