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comparison hubArchiveCreator.xml @ 0:0f3bc17e5ede draft

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author rmarenco
date Wed, 13 Jul 2016 13:22:54 -0400
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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>
9 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>
10 <requirement type="package" version="0.0.1">gtfToGenePred</requirement>
11 <requirement type="package" version="0.0.1">genePredToBed</requirement>
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 $__tool_directory__/hubArchiveCreator.py
33
34 #import json
35
36 #set global data_parameter_dict = {}
37
38 ## Function to retrieve the data of the inputs
39 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})
40 #set false_path = str($input_to_prepare)
41 #set name = $input_to_prepare.name
42
43 #set data_dict = {"name": $name}
44 #silent data_dict.update($extra_data_dict)
45
46 ## Add the ordering by taking the tool form indexes
47 #silent $data_dict.update({"order_index": $order_index + 1})
48
49 #silent $data_parameter_dict.update({$false_path: $data_dict})
50
51 #end def
52
53 #for $i, $f in enumerate( $format )
54 #if $f.formatChoice.format_select == "bam"
55 --bam $f.formatChoice.BAM
56 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
57 #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index})
58 #end if
59 #if $f.formatChoice.format_select == "bed"
60 #if $f.formatChoice.bedChoice.bed_select == "bed"
61 --bed $f.formatChoice.bedChoice.BED
62 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i)
63 #end if
64 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
65 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
66 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i)
67 #end if
68 #end if
69 #if $f.formatChoice.format_select == "bigwig"
70 --bigwig $f.formatChoice.BIGWIG
71 #silent $prepare_json($f.formatChoice.BIGWIG, $i)
72 #end if
73 #if $f.formatChoice.format_select == "gff3"
74 --gff3 $f.formatChoice.GFF3
75 #silent $prepare_json($f.formatChoice.GFF3, $i)
76 #end if
77 #if $f.formatChoice.format_select == "gtf"
78 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
79 --gtf $f.formatChoice.GTF
80 #silent $prepare_json($f.formatChoice.GTF, $i)
81 #end if
82 #end for
83
84 ## Dump the final json
85 #set all_data_json = json.dumps($data_parameter_dict)
86
87 -f $Fasta_File
88 --data_json '$all_data_json'
89
90 -d $__tool_directory__ -e $output.files_path -o $output;
91 ]]></command>
92
93 <inputs>
94 <param
95 format="fasta"
96 name="Fasta_File"
97 type="data"
98 label="Reference genome"
99 />
100 <repeat name="format" title="Formats">
101 <conditional name="formatChoice">
102 <param name="format_select" type="select" label="Format">
103 <option value="bam" selected="true">BAM</option>
104 <option value="bed">BED</option>
105 <option value="bigwig">BIGWIG</option>
106 <option value="gff3">GFF3</option>
107 <option value="gtf">GTF</option>
108 </param>
109
110 <when value="bam">
111 <param
112 format="bam"
113 name="BAM"
114 type="data"
115 label="BAM File"
116 />
117 </when>
118 <when value="bigwig">
119 <param
120 format="bigwig"
121 name="BIGWIG"
122 type="data"
123 label="BIGWIG File"
124 />
125 </when>
126 <when value="gff3">
127 <param
128 format="gff3"
129 name="GFF3"
130 type="data"
131 label="GFF3 File"
132 />
133 </when>
134 <when value="gtf">
135 <param
136 format="gtf"
137 name="GTF"
138 type="data"
139 label="GTF File"
140 />
141 </when>
142 <when value="bed">
143 <conditional name="bedChoice">
144 <param name="bed_select" type="select" label="Bed Choice">
145 <option value="bed" selected="true">Generic BED</option>
146 <option value="bed_simple_repeats_option">BED simple repeats</option>
147 </param>
148 <when value="bed">
149 <param
150 format="bed"
151 name="BED"
152 type="data"
153 label="Generic Bed File Choice"
154 />
155 </when>
156 <when value="bed_simple_repeats_option">
157 <param
158 format="bed"
159 name="BED_simple_repeats"
160 type="data"
161 label="Bed Simple Repeats (Bed4+12) File"
162 />
163 </when>
164 </conditional>
165 </when>
166 </conditional>
167 </repeat>
168 </inputs>
169
170 <outputs>
171 <data format="trackhub" name="output"/>
172 </outputs>
173
174 <tests>
175 <!-- Can also use assert_command to test command -->
176 <!-- Testing GFF3 input -->
177 <test>
178 <param name="Fasta_File" value="dbia3.fa"/>
179 <repeat name="format">
180 <conditional name="formatChoice">
181 <param name="format_select" value="gff3"/>
182 <param name="GFF3" value="augustusDbia3.gff3"/>
183 </conditional>
184 </repeat>
185 <repeat name="format">
186 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/>
187 <!-- TODO: Ask why the tests are not passing with this xml:
188 Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history'
189 <conditional name="formatChoice">
190 <param name="format_select" value="bed"/>
191 <conditional name="bedChoice">
192 <param name="bed_select" value="bed_simple_repeats_option"/>
193 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/>
194 </conditional>
195 </conditional>
196 -->
197 </repeat>
198
199 <output name="output">
200 <assert_contents>
201 <has_text text="myHub"/>
202 </assert_contents>
203 <assert_contents>
204 <has_text text="dbia3_trfBig.bb"/>
205 </assert_contents>
206 <assert_contents>
207 <has_text text="SAODOAii qwwqod92921"/>
208 </assert_contents>
209 </output>
210 </test>
211 <test>
212 <param name="Fasta_File" value="dbia3.fa"/>
213 <param name="GFF3" value="augustusDbia3.gff3"/>
214 <output name="output" file="augustusOutput.html" lines_diff="2">
215 <extra_files type="directory" value="myHub"/>
216 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/>
217 </output>
218 </test>
219 <!-- Testing Generic BED input -->
220 <!-- Testing Bed Simple repeat input -->
221 </tests>
222
223 <help>
224 This Galaxy tool permits to prepare your files to be ready for
225 Assembly Hub visualization.
226 </help>
227 </tool>