Mercurial > repos > rmarenco > hubarchivecreator

comparison hubArchiveCreator.xml @ 10:acc233161f50 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
9:4f9847539a28 10:acc233161f50
29 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] --> 29 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
30 <command detect_errors="exit_code"><![CDATA[ 30 <command detect_errors="exit_code"><![CDATA[
31 mkdir -p $output.extra_files_path; 31 mkdir -p $output.extra_files_path;
32 python $__tool_directory__/hubArchiveCreator.py 32 python $__tool_directory__/hubArchiveCreator.py
33 33
34 ## Ask the user to enter the genome name
35 --genome_name '$genome_name'
36
34 #import json 37 #import json
35 38
36 #set global data_parameter_dict = {} 39 #set global data_parameter_dict = {}
37 40
38 ## Function to retrieve the data of the inputs 41 ## Function to retrieve the data of the inputs
79 --gtf $f.formatChoice.GTF 82 --gtf $f.formatChoice.GTF
80 #silent $prepare_json($f.formatChoice.GTF, $i) 83 #silent $prepare_json($f.formatChoice.GTF, $i)
81 #end if 84 #end if
82 #end for 85 #end for
83 86
87 ## We combine the fasta file dataset name with his false path in a JSON object
88 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
89 -f '$fasta_json'
90
84 ## Dump the final json 91 ## Dump the final json
85 #set all_data_json = json.dumps($data_parameter_dict) 92 #set all_data_json = json.dumps($data_parameter_dict)
86 93
87 -f $Fasta_File
88 --data_json '$all_data_json' 94 --data_json '$all_data_json'
95
96 ## Retrieve the user email
97 --user_email $__user_email__
89 98
90 -d $__tool_directory__ -e $output.files_path -o $output; 99 -d $__tool_directory__ -e $output.files_path -o $output;
91 ]]></command> 100 ]]></command>
92 101
93 <inputs> 102 <inputs>
94 <param 103 <param
104 name="genome_name"
105 type="text"
106 size="30"
107 value="unknown"
108 label="UCSC Genome Browser assembly ID"
109 />
110 <param
95 format="fasta" 111 format="fasta"
96 name="Fasta_File" 112 name="fasta_file"
97 type="data" 113 type="data"
98 label="Reference genome" 114 label="Reference genome"
99 /> 115 />
100 <repeat name="format" title="Formats"> 116 <repeat name="format" title="Formats">
101 <conditional name="formatChoice"> 117 <conditional name="formatChoice">
173 189
174 <tests> 190 <tests>
175 <!-- Can also use assert_command to test command --> 191 <!-- Can also use assert_command to test command -->
176 <!-- Testing GFF3 input --> 192 <!-- Testing GFF3 input -->
177 <test> 193 <test>
178 <param name="Fasta_File" value="dbia3.fa"/> 194 <param name="fasta_file" value="dbia3.fa"/>
179 <repeat name="format"> 195 <repeat name="format">
180 <conditional name="formatChoice"> 196 <conditional name="formatChoice">
181 <param name="format_select" value="gff3"/> 197 <param name="format_select" value="gff3"/>
182 <param name="GFF3" value="augustusDbia3.gff3"/> 198 <param name="GFF3" value="augustusDbia3.gff3"/>
183 </conditional> 199 </conditional>
207 <has_text text="SAODOAii qwwqod92921"/> 223 <has_text text="SAODOAii qwwqod92921"/>
208 </assert_contents> 224 </assert_contents>
209 </output> 225 </output>
210 </test> 226 </test>
211 <test> 227 <test>
212 <param name="Fasta_File" value="dbia3.fa"/> 228 <param name="fasta_file" value="dbia3.fa"/>
213 <param name="GFF3" value="augustusDbia3.gff3"/> 229 <param name="GFF3" value="augustusDbia3.gff3"/>
214 <output name="output" file="augustusOutput.html" lines_diff="2"> 230 <output name="output" file="augustusOutput.html" lines_diff="2">
215 <extra_files type="directory" value="myHub"/> 231 <extra_files type="directory" value="myHub"/>
216 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/> 232 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/>
217 </output> 233 </output>