Mercurial > repos > rmarenco > hubarchivecreator
annotate hubArchiveCreator.xml @ 13:25809f699cb3 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
| author | rmarenco |
|---|---|
| date | Thu, 11 Aug 2016 19:02:29 -0400 |
| parents | d05236b15f81 |
| children | cbd8982c9f51 |
| rev | line source |
|---|---|
|
11
d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
10
diff
changeset
|
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> | |
|
4
1b653b332695
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
3
diff
changeset
|
9 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement> |
|
1b653b332695
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
3
diff
changeset
|
10 <requirement type="package" version="0.0.1">gtfToGenePred</requirement> |
|
1b653b332695
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
3
diff
changeset
|
11 <requirement type="package" version="0.0.1">genePredToBed</requirement> |
| 0 | 12 <requirement type="package" version="1.2">samtools</requirement> |
| 13 <!-- Conda dependencies --> | |
|
11
d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
10
diff
changeset
|
14 <requirement type="package" version="332">ucsc-bedtobigbed</requirement> |
|
d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
10
diff
changeset
|
15 <requirement type="package" version="332">ucsc-fatotwobit</requirement> |
|
d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
10
diff
changeset
|
16 <requirement type="package" version="324">ucsc-genepredtobed</requirement> |
|
13
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
17 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement> |
| 0 | 18 <requirement type="package" version="324">ucsc-gff3togenepred</requirement> |
| 19 <requirement type="package" version="324">ucsc-gtftogenepred</requirement> | |
|
11
d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
10
diff
changeset
|
20 <requirement type="package" version="324">ucsc-twobitinfo</requirement> |
| 0 | 21 <requirement type="package" version="1.3.1">samtools</requirement> |
| 22 </requirements> | |
| 23 | |
| 24 <stdio> | |
| 25 <regex match="^pass1" | |
| 26 source="stderr" | |
| 27 level="log" | |
| 28 description="bedToBigBed"/> | |
| 29 <!-- TODO: Add the case pass1 and 0 chroms --> | |
| 30 <!-- TODO: Add the case pass2 and 0 records or 0 fields --> | |
| 31 </stdio> | |
| 32 | |
| 33 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] --> | |
| 34 <command detect_errors="exit_code"><![CDATA[ | |
| 35 mkdir -p $output.extra_files_path; | |
| 36 python $__tool_directory__/hubArchiveCreator.py | |
| 37 | |
|
10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
38 ## Ask the user to enter the genome name |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
39 --genome_name '$genome_name' |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
40 |
| 0 | 41 #import json |
| 42 | |
| 43 #set global data_parameter_dict = {} | |
| 44 | |
| 45 ## Function to retrieve the data of the inputs | |
| 46 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={}) | |
| 47 #set false_path = str($input_to_prepare) | |
| 48 #set name = $input_to_prepare.name | |
| 49 | |
| 50 #set data_dict = {"name": $name} | |
| 51 #silent data_dict.update($extra_data_dict) | |
| 52 | |
| 53 ## Add the ordering by taking the tool form indexes | |
| 54 #silent $data_dict.update({"order_index": $order_index + 1}) | |
| 55 | |
| 56 #silent $data_parameter_dict.update({$false_path: $data_dict}) | |
| 57 | |
| 58 #end def | |
| 59 | |
| 60 #for $i, $f in enumerate( $format ) | |
| 61 #if $f.formatChoice.format_select == "bam" | |
| 62 --bam $f.formatChoice.BAM | |
| 63 #set bam_index = $f.formatChoice.BAM.metadata.bam_index | |
| 64 #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index}) | |
| 65 #end if | |
| 66 #if $f.formatChoice.format_select == "bed" | |
| 67 #if $f.formatChoice.bedChoice.bed_select == "bed" | |
| 68 --bed $f.formatChoice.bedChoice.BED | |
| 69 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i) | |
| 70 #end if | |
| 71 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" | |
| 72 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats | |
| 73 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i) | |
| 74 #end if | |
| 75 #end if | |
| 76 #if $f.formatChoice.format_select == "bigwig" | |
| 77 --bigwig $f.formatChoice.BIGWIG | |
| 78 #silent $prepare_json($f.formatChoice.BIGWIG, $i) | |
| 79 #end if | |
| 80 #if $f.formatChoice.format_select == "gff3" | |
| 81 --gff3 $f.formatChoice.GFF3 | |
| 82 #silent $prepare_json($f.formatChoice.GFF3, $i) | |
| 83 #end if | |
| 84 #if $f.formatChoice.format_select == "gtf" | |
| 85 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 | |
| 86 --gtf $f.formatChoice.GTF | |
| 87 #silent $prepare_json($f.formatChoice.GTF, $i) | |
| 88 #end if | |
| 89 #end for | |
| 90 | |
|
10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
91 ## We combine the fasta file dataset name with his false path in a JSON object |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
92 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name}) |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
93 -f '$fasta_json' |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
94 |
| 0 | 95 ## Dump the final json |
| 96 #set all_data_json = json.dumps($data_parameter_dict) | |
| 97 | |
| 98 --data_json '$all_data_json' | |
| 99 | |
|
10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
100 ## Retrieve the user email |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
101 --user_email $__user_email__ |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
102 |
|
13
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
103 -d $__tool_directory__ |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
104 |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
105 -e $output.files_path |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
106 |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
107 $advanced_options.debug_mode |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
108 |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
109 -o $output; |
| 0 | 110 ]]></command> |
| 111 | |
| 112 <inputs> | |
| 113 <param | |
|
10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
114 name="genome_name" |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
115 type="text" |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
116 size="30" |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
117 value="unknown" |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
118 label="UCSC Genome Browser assembly ID" |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
119 /> |
|
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
120 <param |
| 0 | 121 format="fasta" |
|
10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
122 name="fasta_file" |
| 0 | 123 type="data" |
| 124 label="Reference genome" | |
| 125 /> | |
| 126 <repeat name="format" title="Formats"> | |
| 127 <conditional name="formatChoice"> | |
| 128 <param name="format_select" type="select" label="Format"> | |
| 129 <option value="bam" selected="true">BAM</option> | |
| 130 <option value="bed">BED</option> | |
| 131 <option value="bigwig">BIGWIG</option> | |
| 132 <option value="gff3">GFF3</option> | |
| 133 <option value="gtf">GTF</option> | |
| 134 </param> | |
| 135 | |
| 136 <when value="bam"> | |
| 137 <param | |
| 138 format="bam" | |
| 139 name="BAM" | |
| 140 type="data" | |
| 141 label="BAM File" | |
| 142 /> | |
| 143 </when> | |
| 144 <when value="bigwig"> | |
| 145 <param | |
| 146 format="bigwig" | |
| 147 name="BIGWIG" | |
| 148 type="data" | |
| 149 label="BIGWIG File" | |
| 150 /> | |
| 151 </when> | |
| 152 <when value="gff3"> | |
| 153 <param | |
| 154 format="gff3" | |
| 155 name="GFF3" | |
| 156 type="data" | |
| 157 label="GFF3 File" | |
| 158 /> | |
| 159 </when> | |
| 160 <when value="gtf"> | |
| 161 <param | |
| 162 format="gtf" | |
| 163 name="GTF" | |
| 164 type="data" | |
| 165 label="GTF File" | |
| 166 /> | |
| 167 </when> | |
| 168 <when value="bed"> | |
| 169 <conditional name="bedChoice"> | |
| 170 <param name="bed_select" type="select" label="Bed Choice"> | |
|
11
d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
10
diff
changeset
|
171 <option value="bed" selected="true">BED Generic (bed3+)</option> |
|
d05236b15f81
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
rmarenco
parents:
10
diff
changeset
|
172 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> |
| 0 | 173 </param> |
| 174 <when value="bed"> | |
| 175 <param | |
| 176 format="bed" | |
| 177 name="BED" | |
| 178 type="data" | |
| 179 label="Generic Bed File Choice" | |
| 180 /> | |
| 181 </when> | |
| 182 <when value="bed_simple_repeats_option"> | |
| 183 <param | |
| 184 format="bed" | |
| 185 name="BED_simple_repeats" | |
| 186 type="data" | |
| 187 label="Bed Simple Repeats (Bed4+12) File" | |
| 188 /> | |
| 189 </when> | |
| 190 </conditional> | |
| 191 </when> | |
| 192 </conditional> | |
| 193 </repeat> | |
|
13
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
194 <conditional name="advanced_options"> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
195 <param name="advanced_options_selector" type="select" label="Advanced options"> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
196 <option value="off" selected="true">Hide advanced options</option> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
197 <option value="on">Display advanced options</option> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
198 </param> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
199 <!-- TODO: Avoid redundancy here --> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
200 <when value="on"> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
201 <param name="debug_mode" type="boolean" |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
202 label="Activate debug mode" checked="false" |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
203 truevalue="--debug_mode" falsevalue=""> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
204 <help> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
205 Use this option if you are a G-OnRamp developer |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
206 </help> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
207 </param> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
208 </when> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
209 <when value="off"> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
210 <param name="debug_mode" type="hidden" |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
211 value=""> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
212 </param> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
213 </when> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
214 </conditional> |
|
25809f699cb3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
rmarenco
parents:
11
diff
changeset
|
215 </inputs> |
| 0 | 216 |
| 217 <outputs> | |
| 218 <data format="trackhub" name="output"/> | |
| 219 </outputs> | |
| 220 | |
| 221 <tests> | |
| 222 <!-- Can also use assert_command to test command --> | |
| 223 <!-- Testing GFF3 input --> | |
| 224 <test> | |
|
10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
225 <param name="fasta_file" value="dbia3.fa"/> |
| 0 | 226 <repeat name="format"> |
| 227 <conditional name="formatChoice"> | |
| 228 <param name="format_select" value="gff3"/> | |
| 229 <param name="GFF3" value="augustusDbia3.gff3"/> | |
| 230 </conditional> | |
| 231 </repeat> | |
| 232 <repeat name="format"> | |
| 233 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> | |
| 234 <!-- TODO: Ask why the tests are not passing with this xml: | |
| 235 Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history' | |
| 236 <conditional name="formatChoice"> | |
| 237 <param name="format_select" value="bed"/> | |
| 238 <conditional name="bedChoice"> | |
| 239 <param name="bed_select" value="bed_simple_repeats_option"/> | |
| 240 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> | |
| 241 </conditional> | |
| 242 </conditional> | |
| 243 --> | |
| 244 </repeat> | |
| 245 | |
| 246 <output name="output"> | |
| 247 <assert_contents> | |
| 248 <has_text text="myHub"/> | |
| 249 </assert_contents> | |
| 250 <assert_contents> | |
| 251 <has_text text="dbia3_trfBig.bb"/> | |
| 252 </assert_contents> | |
| 253 <assert_contents> | |
| 254 <has_text text="SAODOAii qwwqod92921"/> | |
| 255 </assert_contents> | |
| 256 </output> | |
| 257 </test> | |
| 258 <test> | |
|
10
acc233161f50
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
rmarenco
parents:
4
diff
changeset
|
259 <param name="fasta_file" value="dbia3.fa"/> |
| 0 | 260 <param name="GFF3" value="augustusDbia3.gff3"/> |
| 261 <output name="output" file="augustusOutput.html" lines_diff="2"> | |
| 262 <extra_files type="directory" value="myHub"/> | |
| 263 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/> | |
| 264 </output> | |
| 265 </test> | |
| 266 <!-- Testing Generic BED input --> | |
| 267 <!-- Testing Bed Simple repeat input --> | |
| 268 </tests> | |
| 269 | |
| 270 <help> | |
| 271 This Galaxy tool permits to prepare your files to be ready for | |
| 272 Assembly Hub visualization. | |
| 273 </help> | |
| 274 </tool> |