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comparison tapdance.xml @ 0:1437a2df99c0

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author jesse-erdmann
date Fri, 09 Dec 2011 11:56:56 -0500
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1 <tool id="tapdance_runner" name="TAPDANCE" version="1.0" force_history_refresh="True">
2 <description>A tool for identifying Common Insertion Sites</description>
3 <command interpreter="perl">tapdance_runner.pl -index $index -index_id $index.id -index_path $index.extra_files_path
4 #if $predef.predef_select.__str__() == 'PREDEF':
5 -s $predef.seqs -b $predef.bar2lib -pn $userEmail$predef.proj_name -config $predef.config
6 #else
7 ## INPUT
8 #if $predef.start_point.start_select.__str__() == 'sequences':
9 -s $predef.start_point.seqs -b $predef.start_point.bar2lib -bowtieIdx $predef.start_point.genomeIdx -pn $userEmail$predef.start_point.proj_name
10 #for $entry in $predef.start_point.mutagens
11 #if $entry.mutagen.mutagen_select.__str__() == 'CUSTOM':
12 -mutagen $entry.mutagen.mutagen_custom.__str__()
13 #else
14 -mutagen $entry.mutagen.mutagen_select.__str__()
15 #end if
16 #end for
17 #end if
18 #if $predef.start_point.start_select.__str__() == 'single_project':
19 -pn $predef.start_point.cis_project.__str__()
20 #end if
21 #if $predef.start_point.start_select.__str__() == 'multiple_projects':
22 -pn $userEmail$predef.start_point.proj_name -merge $predef.start_point.merge_projects.__str__()
23 #end if
24
25 ## OUTPUT
26 #if $predef.start_point.start_select.__str__() != 'single_project':
27 -pb $projBed -projectBedId $projBed.id
28 ##-ps $projSum -projectSummaryId $projSum.id -pv $projVis -projectVisId $projVis.id
29 #end if
30 #if $predef.results.result_select.__str__() == 'cis':
31 -cw $cisWig -cwid $cisWig.id -cwpath $__new_file_path__
32 ##-cs $cisSum -cisSumId $cisSum.id
33 -lib_pct $predef.results.cis_params.lib_pct -CIS_tot_p $predef.results.cis_params.CIS_tot_p -CIS_lib_p $predef.results.cis_params.CIS_lib_p -CIS_reg_p $predef.results.cis_params.CIS_reg_p -coCIS_thresh $predef.results.cis_params.coCIS_thresh
34 #if $predef.results.metadata.metadata_select.__str__() == 'CUSTOM':
35 -m $predef.results.metadata.metadata_custom.__str__()
36 #end if
37 #if $predef.results.annotation.annotation_select.__str__() == 'CUSTOM':
38 -m $predef.results.annotation.annotation_file.__str__()
39 #end if
40 #for $entry in $predef.results.omitChroms
41 -o $entry.omitChrom.__str__()
42 #end for
43 #else
44 -no_cis
45 #end if
46 #end if
47 </command>
48 <inputs>
49 <conditional name="predef">
50 <param name="predef_select" type="select" label="Enter values below or use a predefined config file?">
51 <option value="CUSTOM">Enter values below</option>
52 <option value="PREDEF">Use predefined config file</option>
53 </param>
54 <when value="PREDEF">
55 <param name="proj_name" type="text" label="New Project Name" optional="false"/>
56 <param name="seqs" type="data" format="fastq,fasta,tabular" label="Sequence File" optional="false"/>
57 <param name="bar2lib" type="data" format="tabular" label="Barcode to Library Map" optional="false"/>
58 <param name="config" type="data" format="text" label="Predefined Config File" optional="false"/>
59 <conditional name="metadata">
60 <param name="metadata_select" type="select" label="Library Metadata" help="Automatic metadata generation or custom">
61 <option value="AUTOMATIC">Generate default</option>
62 <option value="CUSTOM">Use uploaded data</option>
63 </param>
64 <when value="AUTOMATIC">
65 <param name="metadata_custom" type="hidden" value=""/>
66 </when>
67 <when value="CUSTOM">
68 <param name="metadata_custom" type="data" format="tabular" label="Metadata Input" help="Library/Tag pairs, tab delmited"/>
69 </when>
70 </conditional>
71 </when>
72 <when value="CUSTOM">
73 <conditional name="start_point">
74 <param name="start_select" type="select" label="Starting Point">
75 <option value="sequences">FASTQ or FASTA</option>
76 <option value="single_project">Existing Project</option>
77 <option value="multiple_projects">Merge Multiple Projects</option>
78 </param>
79 <when value="sequences">
80 <param name="proj_name" type="text" label="New Project Name" optional="false"/>
81 <param name="seqs" type="data" format="fastq,fasta,tabular" label="Sequence File" optional="false"/>
82 <param name="bar2lib" type="data" format="tabular" label="Barcode to Library Map" optional="false"/>
83 <repeat name="mutagens" title="Mutagen(s)" min="1">
84 <conditional name="mutagen">
85 <param name="mutagen_select" type="select" label="Mutagen matching" help="Choose the appropriate match for this experiment">
86 <option value="TGTATGTAAACTTCCGACTTCAACTG">Sleeping Beauty Example, TGTATGTAAACTTCCGACTTCAACTG</option>
87 <option value="CUSTOM">Other</option>
88 </param>
89 <when value="TGTATGTAAACTTCCGACTTCAACTG">
90 <param name="mutagen_custom" type="hidden" value=""/>
91 </when>
92 <when value="CUSTOM">
93 <param name="mutagen_custom" type="text" label="Mutagen Sequence" help="Enter the sequence to match as the mutagen, '_' may be used to match any single base. E.G. _GTATGTAAACTTCCGACTTCAACTG would match both AGTATGTAAACTTCCGACTTCAACTG and TGTATGTAAACTTCCGACTTCAACTG"/>
94 </when>
95 </conditional>
96 </repeat>
97 <param name="genomeIdx" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact help@msi.umn.edu">
98 <options from_file="bowtie_indices.loc">
99 <column name="value" index="3" />
100 <column name="name" index="0" />
101 </options>
102 </param>
103 </when>
104 <when value="single_project">
105 <param name="proj_source" type="data" format="tabular" label="Available Projects File" help="If you do not have a project list file, select the project type 'Generate Project List'"/>
106 <param name="cis_project" type="select" label="Project" data_ref="proj_source">
107 <options from_dataset="proj_source">
108 <column name="name" index="1"/>
109 <column name="value" index="0"/>
110 </options>
111 </param>
112 </when>
113 <when value="multiple_projects">
114 <param name="proj_name" type="text" label="New Project Name" optional="false"/>
115 <param name="proj_source" type="data" format="tabular" label="Available Projects File" help="If you do not have a project list file, select the project type 'Generate Project List'"/>
116 <param name="merge_projects" type="select" multiple="true" label="Projects to Merge" data_ref="proj_source">
117 <options from_dataset="proj_source">
118 <column name="name" index="1"/>
119 <column name="value" index="0"/>
120 </options>
121 </param>
122 </when>
123 </conditional>
124 <conditional name="results">
125 <param name="result_select" type="select" label="Desired Results">
126 <option value="cis">CIS calls</option>
127 <option value="inserts">Inserts Only (useful for QC)</option>
128 </param>
129 <when value="inserts">
130 <param type="hidden" value="" name="inserts_only"/>
131 </when>
132 <when value="cis">
133 <conditional name="metadata">
134 <param name="metadata_select" type="select" label="Library Metadata" help="Automatic metadata generation or custom">
135 <option value="AUTOMATIC">Generate default</option>
136 <option value="CUSTOM">Use uploaded data</option>
137 </param>
138 <when value="AUTOMATIC">
139 <param name="metadata_custom" type="hidden" value=""/>
140 </when>
141 <when value="CUSTOM">
142 <param name="metadata_custom" type="data" format="tabular" label="Metadata Input" help="Library/Tag pairs, tab delmited"/>
143 </when>
144 </conditional>
145 <repeat name="omitChroms" title="Chromosomes to Omit" help="The chromosome of the donor concatemer is often omitted">
146 <param type="text" name="omitChrom" label="Chromosome Label" help="e.g. chr1"/>
147 </repeat>
148 <conditional name="annotation">
149 <param name="annotation_select" label="Annotation Features" type="select" help="Specify an interval file containing genomic features to annotate CIS calls">
150 <option value="DEFAULT">Default: mm9 refSeq genes</option>
151 <option value="CUSTOM">Specify interval file</option>
152 </param>
153 <when value="DEFAULT">
154 <param type="hidden" name="annotation_file" value=""/>
155 </when>
156 <when value="CUSTOM">
157 <param type="data" format="interval" name="annotation_file" label="Annotation Source"/>
158 </when>
159 </conditional>
160 <conditional name="cis_params">
161 <param name="cis_params_select" type="select" label="CIS calling parameters">
162 <option value="default">Use defaults</option>
163 <option value="custom">Specify values</option>
164 </param>
165 <when value="default">
166 <param type="hidden" value="0.0001" name="lib_pct"/>
167 <param type="hidden" value="0.05" name="CIS_tot_p"/>
168 <param type="hidden" value="0.05" name="CIS_lib_p"/>
169 <param type="hidden" value="0.05" name="CIS_reg_p"/>
170 <param type="hidden" value="0.0001" name="coCIS_thresh"/>
171 </when>
172 <when value="custom">
173 <param type="float" value="0.0001" name="lib_pct" label="Library Percent"/>
174 <param type="float" value="0.05" name="CIS_tot_p" label="CIS Total pvalue"/>
175 <param type="float" value="0.05" name="CIS_lib_p" label="CIS Library pvalue"/>
176 <param type="float" value="0.05" name="CIS_reg_p" label="CIS Region pvalue"/>
177 <param type="float" value="0.0001" name="coCIS_thresh" label="coCIS Threshold"/>
178 </when>
179 </conditional>
180 </when>
181 </conditional>
182 </when>
183 </conditional>
184 </inputs>
185 <outputs>
186 <data format="html" name="index" label="TAPDANCE Results"/>
187 <data format="bed" name="projBed" label="Non Redundant Inserts BED" visible="false">
188 <filter>(
189 predef['predef_select'] == 'PREDEF' or
190 predef['start_point']['start_select'] != 'single_project'
191 )
192 </filter>
193 </data>
194 <!--
195 <data format="txt" name="projSum" label="Summary" hidden="true">
196 <filter>(
197 predef['predef_select'] == 'PREDEF' or
198 predef['start_point']['start_select'] == 'sequences'
199 )
200 </filter>
201 </data>
202 <data format="pdf" name="projVis" label="Insert Graphs">
203 <filter>(predef['predef_select'] == 'PREDEF' or predef['start_point']['start_select'] != 'single_project')</filter>
204 </data>
205 -->
206 <!-- due to optional start with seqs, can no longer use the seqs metadata as a source for cisWig metadata -->
207 <data format="wig" name="cisWig" label="CIS WIG">
208 <filter>(
209 predef['predef_select'] == 'PREDEF' or
210 predef['results']['result_select'] == 'cis'
211 )
212 </filter>
213 </data>
214 <!--
215 <data format="txt" name="cisSum" label="CIS Summary">
216 <filter>(
217 predef['predef_select'] == 'PREDEF' or
218 predef['results']['result_select'] == 'cis'
219 )
220 </filter>
221 </data>
222 -->
223 </outputs>
224 <!--<code file="tapdance_index.py">
225 <hook exec_after_process="exec_after_completion" />
226 </code>-->
227 <help>
228 See full help at https://sourceforge.net/p/tapdancebio/wiki/
229
230 `Report a Problem`_
231
232 .. _Report a Problem: https://sourceforge.net/p/tapdancebio/tickets/new/
233
234 </help>
235 </tool>