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comparison crossmap.xml @ 31:ebcd672e9072 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
author yhoogstrate
date Thu, 12 Nov 2015 10:30:40 -0500
parents 179bf64d12ef
children 00a4682c94bc
comparison
equal deleted inserted replaced
30:179bf64d12ef 31:ebcd672e9072
14 14
15 <version_command>python $CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> 15 <version_command>python $CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
16 16
17 <command><!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: --> 17 <command><!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: -->
18 python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py 18 python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py
19 ${input_format.replace("sam","bam")} 19 ${multiple.input_format.replace("sam","bam")}
20 20
21 #if $input_format == "vcf" and $seq_source.index_source == "cached" 21 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
22 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up --> 22 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
23 "${filter(lambda x: str( x[1] ) == str($seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" 23 "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
24 #else 24 #else
25 "$seq_source.input_chain" 25 "$multiple.seq_source.input_chain"
26 #end if 26 #end if
27 27
28 #if $input_format in ["bam", "sam"] 28 #if $multiple.input_format in ["bam", "sam"]
29 -m $insert_size 29 -m $multiple.insert_size
30 -s $insert_size_stdev 30 -s $multiple.insert_size_stdev
31 -t $insert_size_fold 31 -t $multiple.insert_size_fold
32 #end if 32 #end if
33 33
34 "$seq_source.input" 34 "$multiple.seq_source.input"
35 35
36 #if $input_format == "vcf" 36 #if $multiple.input_format == "vcf"
37 "$seq_source.input_fasta" 37 "$multiple.seq_source.input_fasta"
38 #end if 38 #end if
39 39
40 #if str($include_fails) == "True" 40 #if str($multiple.include_fails) == "True"
41 > 41 >
42 #end if 42 #end if
43 43
44 "$output" 44 "$output"
45 45
46 #if $input_format in ["bam", "sam"] 46 #if $multiple.input_format in ["bam", "sam"]
47 ; mv "${output}.${input_format}" "$output" 47 ; mv "${output}.${multiple.input_format}" "$output"
48 ; mv "${output}.unmap.${input_format}" "$output_unmapped" 48 ; mv "${output}.unmap.${multiple.input_format}" "$output_unmapped"
49 #else if $input_format in ["vcf"] 49 #else if $multiple.input_format in ["vcf"]
50 ; mv "${output}" "$output" 50 ; mv "${output}" "$output"
51 ; mv "${output}.unmap" "$output_unmapped" 51 ; mv "${output}.unmap" "$output_unmapped"
52 #else if $input_format in ["wig", "bigwig"] 52 #else if $multiple.input_format in ["wig", "bigwig"]
53 ; mv "${output}.bw" "$output" 53 ; mv "${output}.bw" "$output"
54 ; mv "${output}.sorted.bgr" "$output2" 54 ; mv "${output}.sorted.bgr" "$output2"
55 #end if 55 #end if
56 </command> 56 </command>
57 57
58 <inputs> 58 <inputs>
59 <param name="input_format" type="select" label="Convert a file of the following format"> 59 <conditional name="multiple">
60 <option value="bam">BAM</option> 60 <param name="input_format" type="select" label="Convert a file of the following format">
61 <option value="sam">SAM</option> 61 <option value="bam">BAM</option>
62 <option value="bed">BED or BED-like</option> 62 <option value="sam">SAM</option>
63 <option value="bigwig">BigWig</option> 63 <option value="bed">BED or BED-like</option>
64 <option value="gff">GFF or GTF</option> 64 <option value="bigwig">BigWig</option>
65 <option value="vcf">VCF</option> 65 <option value="gff">GFF or GTF</option>
66 <option value="wig">Wiggle or bedGraph</option> 66 <option value="vcf">VCF</option>
67 </param> 67 <option value="wig">Wiggle or bedGraph</option>
68 <when value="bam"> 68 </param>
69 <conditional name="seq_source"> 69 <when value="bam">
70 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> 70 <conditional name="seq_source">
71 <option value="cached">Local data (in galaxy)</option> 71 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
72 <option value="history">From History</option> 72 <option value="cached">Local data (in galaxy)</option>
73 </param> 73 <option value="history">From History</option>
74 </param>
75 <when value="cached">
76 <param type="data" format="bam" name="input" label="BAM/SAM file">
77 <validator type="unspecified_build" />
78 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
79 </param>
80 <param name="input_chain" type="select" label="Lift Over To">
81 <options from_file="liftOver.loc">
82 <column name="name" index="1"/>
83 <column name="value" index="2"/>
84 <column name="dbkey" index="0"/>
85 <filter type="data_meta" ref="input" key="dbkey" column="0" />
86 </options>
87 </param>
88 </when>
89 <when value="history">
90 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
91 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
92 </when>
93 </conditional>
94
95 <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" />
96 <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" />
97 <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" />
98
99 <param name="include_fails" type="hidden" tvalue="False" />
100 </when>
101 <when value="sam"><!-- BAM and SAM are exactly the same conditions, but they need to be separate to get the proper output format -->
102 <conditional name="seq_source">
103 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
104 <option value="cached">Local data (in galaxy)</option>
105 <option value="history">From History</option>
106 </param>
107 <when value="cached">
108 <param type="data" format="sam" name="input" label="BAM/SAM file">
109 <validator type="unspecified_build" />
110 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
111 </param>
112 <param name="input_chain" type="select" label="Lift Over To">
113 <options from_file="liftOver.loc">
114 <column name="name" index="1"/>
115 <column name="value" index="2"/>
116 <column name="dbkey" index="0"/>
117 <filter type="data_meta" ref="input" key="dbkey" column="0" />
118 </options>
119 </param>
120 </when>
121 <when value="history">
122 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
123 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
124 </when>
125 </conditional>
126
127 <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" />
128 <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" />
129 <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" />
130
131 <param name="include_fails" type="hidden" tvalue="False" />
132 </when>
133 <when value="bed">
134 <conditional name="seq_source">
135 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
136 <option value="cached">Local data (in galaxy)</option>
137 <option value="history">From History</option>
138 </param>
139 <when value="cached">
140 <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.">
141 <validator type="unspecified_build" />
142 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
143 </param>
144 <param name="input_chain" type="select" label="Lift Over To">
145 <options from_file="liftOver.loc">
146 <column name="name" index="1"/>
147 <column name="value" index="2"/>
148 <column name="dbkey" index="0"/>
149 <filter type="data_meta" ref="input" key="dbkey" column="0" />
150 </options>
151 </param>
152 </when>
153 <when value="history">
154 <param type="data" format="bed" name="input" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." />
155 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
156 </when>
157 </conditional>
158
159 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" />
160 </when>
161 <when value="bigwig">
162 <conditional name="seq_source">
163 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
164 <option value="cached">Local data (in galaxy)</option>
165 <option value="history">From History</option>
166 </param>
167 <when value="cached">
168 <param format="bigwig" name="input" type="data" label="BigWig file">
169 <validator type="unspecified_build" />
170 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
171 </param>
172 <param name="input_chain" type="select" label="Lift Over To">
173 <options from_file="liftOver.loc">
174 <column name="name" index="1"/>
175 <column name="value" index="2"/>
176 <column name="dbkey" index="0"/>
177 <filter type="data_meta" ref="input" key="dbkey" column="0" />
178 </options>
179 </param>
180 </when>
181 <when value="history">
182 <param type="data" format="bigwig" name="input" label="BigWig file" />
183 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
184 </when>
185 </conditional>
186
187 <param name="include_fails" type="hidden" tvalue="False" />
188 </when>
189 <when value="gff">
190 <conditional name="seq_source">
191 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
192 <option value="cached">Local data (in galaxy)</option>
193 <option value="history">From History</option>
194 </param>
195 <when value="cached">
196 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
197 <validator type="unspecified_build" />
198 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
199 </param>
200 <param name="input_chain" type="select" label="Lift Over To">
201 <options from_file="liftOver.loc">
202 <column name="name" index="1"/>
203 <column name="value" index="2"/>
204 <column name="dbkey" index="0"/>
205 <filter type="data_meta" ref="input" key="dbkey" column="0" />
206 </options>
207 </param>
208 </when>
209 <when value="history">
210 <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file" />
211 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
212 </when>
213 </conditional>
214
215 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" />
216 </when>
217 <when value="vcf">
218 <conditional name="seq_source">
219 <param name="index_source" type="select" label="Source for LiftOver Data">
220 <option value="cached">Local data (in galaxy)</option>
221 <option value="history_chain">Chain file from History</option>
222 <option value="history_all">Chain &amp; FASTA files from History</option>
223 </param>
224
74 <when value="cached"> 225 <when value="cached">
75 <param type="data" format="bam" name="input" label="BAM/SAM file"> 226 <param type="data" format="vcf" name="input" label="VCF file">
227 <validator type="unspecified_build" />
228 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
229 </param>
230
231 <!-- automatically fetch a FASTA file from the same DBKEY as the chain file -->
232 <param name="input_chain" type="select" label="Lift Over To (Chain file)">
233 <options from_file="liftOver.loc">
234 <column name="name" index="1" />
235 <column name="value" index="1" /><!-- It is not possible to send the *.chain file as value, and obtain the 2nd dbkey as parameter via a filter -->
236 <column name="dbkey" index="0" />
237 <filter type="data_meta" ref="input" key="dbkey" column="0" />
238 </options>
239 </param>
240
241 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
242 <options from_file="all_fasta.loc">
243 <column name="name" index="2"/>
244 <column name="value" index="3"/>
245 <column name="dbkey" index="1"/>
246 <filter type="param_value" ref="input_chain" column="1" />
247 </options>
248 </param>
249 </when>
250
251 <when value="history_chain">
252 <param type="data" format="vcf" name="input" label="VCF file">
253 <validator type="unspecified_build" />
254 <validator type="dataset_metadata_in_file" filename="all_fasta.loc" metadata_name="dbkey" metadata_column="1" message="LiftOver mapping (FASTA file) is not available for the specified build." />
255 </param>
256 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
257 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
258 <options from_file="all_fasta.loc">
259 <column name="name" index="2"/>
260 <column name="value" index="3"/>
261 <column name="dbkey" index="1"/>
262 </options>
263 </param>
264 </when>
265
266 <when value="history_all">
267 <param type="data" format="vcf" name="input" label="VCF file" />
268 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
269 <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file" />
270 </when>
271 </conditional>
272
273 <param name="include_fails" type="hidden" tvalue="False" />
274 </when>
275 <when value="wig">
276 <conditional name="seq_source">
277 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
278 <option value="cached">Local data (in galaxy)</option>
279 <option value="history">From History</option>
280 </param>
281 <when value="cached">
282 <param format="wig" name="input" type="data" label="Wiggle file">
76 <validator type="unspecified_build" /> 283 <validator type="unspecified_build" />
77 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> 284 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
78 </param> 285 </param>
79 <param name="input_chain" type="select" label="Lift Over To"> 286 <param name="input_chain" type="select" label="Lift Over To">
80 <options from_file="liftOver.loc"> 287 <options from_file="liftOver.loc">
84 <filter type="data_meta" ref="input" key="dbkey" column="0" /> 291 <filter type="data_meta" ref="input" key="dbkey" column="0" />
85 </options> 292 </options>
86 </param> 293 </param>
87 </when> 294 </when>
88 <when value="history"> 295 <when value="history">
89 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" /> 296 <param format="wig" name="input" type="data" label="Wiggle file" />
90 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> 297 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
91 </when> 298 </when>
92 </conditional> 299 </conditional>
93 300
94 <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" /> 301 <param name="include_fails" type="hidden" tvalue="False" />
95 <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" /> 302 </when>
96 <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" /> 303 </conditional>
97
98 <param name="include_fails" type="hidden" tvalue="False" />
99 </when>
100 <when value="sam"><!-- BAM and SAM are exactly the same conditions, but they need to be separate to get the proper output format -->
101 <conditional name="seq_source">
102 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
103 <option value="cached">Local data (in galaxy)</option>
104 <option value="history">From History</option>
105 </param>
106 <when value="cached">
107 <param type="data" format="sam" name="input" label="BAM/SAM file">
108 <validator type="unspecified_build" />
109 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
110 </param>
111 <param name="input_chain" type="select" label="Lift Over To">
112 <options from_file="liftOver.loc">
113 <column name="name" index="1"/>
114 <column name="value" index="2"/>
115 <column name="dbkey" index="0"/>
116 <filter type="data_meta" ref="input" key="dbkey" column="0" />
117 </options>
118 </param>
119 </when>
120 <when value="history">
121 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
122 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
123 </when>
124 </conditional>
125
126 <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" />
127 <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" />
128 <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" />
129
130 <param name="include_fails" type="hidden" tvalue="False" />
131 </when>
132 <when value="bed">
133 <conditional name="seq_source">
134 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
135 <option value="cached">Local data (in galaxy)</option>
136 <option value="history">From History</option>
137 </param>
138 <when value="cached">
139 <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.">
140 <validator type="unspecified_build" />
141 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
142 </param>
143 <param name="input_chain" type="select" label="Lift Over To">
144 <options from_file="liftOver.loc">
145 <column name="name" index="1"/>
146 <column name="value" index="2"/>
147 <column name="dbkey" index="0"/>
148 <filter type="data_meta" ref="input" key="dbkey" column="0" />
149 </options>
150 </param>
151 </when>
152 <when value="history">
153 <param type="data" format="bed" name="input" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." />
154 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
155 </when>
156 </conditional>
157
158 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" />
159 </when>
160 <when value="bigwig">
161 <conditional name="seq_source">
162 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
163 <option value="cached">Local data (in galaxy)</option>
164 <option value="history">From History</option>
165 </param>
166 <when value="cached">
167 <param format="bigwig" name="input" type="data" label="BigWig file">
168 <validator type="unspecified_build" />
169 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
170 </param>
171 <param name="input_chain" type="select" label="Lift Over To">
172 <options from_file="liftOver.loc">
173 <column name="name" index="1"/>
174 <column name="value" index="2"/>
175 <column name="dbkey" index="0"/>
176 <filter type="data_meta" ref="input" key="dbkey" column="0" />
177 </options>
178 </param>
179 </when>
180 <when value="history">
181 <param type="data" format="bigwig" name="input" label="BigWig file" />
182 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
183 </when>
184 </conditional>
185
186 <param name="include_fails" type="hidden" tvalue="False" />
187 </when>
188 <when value="gff">
189 <conditional name="seq_source">
190 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
191 <option value="cached">Local data (in galaxy)</option>
192 <option value="history">From History</option>
193 </param>
194 <when value="cached">
195 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
196 <validator type="unspecified_build" />
197 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
198 </param>
199 <param name="input_chain" type="select" label="Lift Over To">
200 <options from_file="liftOver.loc">
201 <column name="name" index="1"/>
202 <column name="value" index="2"/>
203 <column name="dbkey" index="0"/>
204 <filter type="data_meta" ref="input" key="dbkey" column="0" />
205 </options>
206 </param>
207 </when>
208 <when value="history">
209 <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file" />
210 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
211 </when>
212 </conditional>
213
214 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" />
215 </when>
216 <when value="vcf">
217 <conditional name="seq_source">
218 <param name="index_source" type="select" label="Source for LiftOver Data">
219 <option value="cached">Local data (in galaxy)</option>
220 <option value="history_chain">Chain file from History</option>
221 <option value="history_all">Chain &amp; FASTA files from History</option>
222 </param>
223
224 <when value="cached">
225 <param type="data" format="vcf" name="input" label="VCF file">
226 <validator type="unspecified_build" />
227 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
228 </param>
229
230 <!-- automatically fetch a FASTA file from the same DBKEY as the chain file -->
231 <param name="input_chain" type="select" label="Lift Over To (Chain file)">
232 <options from_file="liftOver.loc">
233 <column name="name" index="1" />
234 <column name="value" index="1" /><!-- It is not possible to send the *.chain file as value, and obtain the 2nd dbkey as parameter via a filter -->
235 <column name="dbkey" index="0" />
236 <filter type="data_meta" ref="input" key="dbkey" column="0" />
237 </options>
238 </param>
239
240 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
241 <options from_file="all_fasta.loc">
242 <column name="name" index="2"/>
243 <column name="value" index="3"/>
244 <column name="dbkey" index="1"/>
245 <filter type="param_value" ref="input_chain" column="1" />
246 </options>
247 </param>
248 </when>
249
250 <when value="history_chain">
251 <param type="data" format="vcf" name="input" label="VCF file">
252 <validator type="unspecified_build" />
253 <validator type="dataset_metadata_in_file" filename="all_fasta.loc" metadata_name="dbkey" metadata_column="1" message="LiftOver mapping (FASTA file) is not available for the specified build." />
254 </param>
255 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
256 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
257 <options from_file="all_fasta.loc">
258 <column name="name" index="2"/>
259 <column name="value" index="3"/>
260 <column name="dbkey" index="1"/>
261 </options>
262 </param>
263 </when>
264
265 <when value="history_all">
266 <param type="data" format="vcf" name="input" label="VCF file" />
267 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
268 <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file" />
269 </when>
270 </conditional>
271
272 <param name="include_fails" type="hidden" tvalue="False" />
273 </when>
274 <when value="wig">
275 <conditional name="seq_source">
276 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
277 <option value="cached">Local data (in galaxy)</option>
278 <option value="history">From History</option>
279 </param>
280 <when value="cached">
281 <param format="wig" name="input" type="data" label="Wiggle file">
282 <validator type="unspecified_build" />
283 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
284 </param>
285 <param name="input_chain" type="select" label="Lift Over To">
286 <options from_file="liftOver.loc">
287 <column name="name" index="1"/>
288 <column name="value" index="2"/>
289 <column name="dbkey" index="0"/>
290 <filter type="data_meta" ref="input" key="dbkey" column="0" />
291 </options>
292 </param>
293 </when>
294 <when value="history">
295 <param format="wig" name="input" type="data" label="Wiggle file" />
296 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
297 </when>
298 </conditional>
299
300 <param name="include_fails" type="hidden" tvalue="False" />
301 </when>
302 </inputs> 304 </inputs>
303 305
304 <outputs> 306 <outputs>
305 <data format="text" name="output" label="${tool.name} on ${on_string}"> 307 <data format="text" name="output" label="${tool.name} on ${on_string}">
306 <change_format> 308 <change_format>
307 <when input="input_format" value="bam" format="bam" /> 309 <when input="multiple.input_format" value="bam" format="bam" />
308 <when input="input_format" value="sam" format="sam" /> 310 <when input="multiple.input_format" value="sam" format="sam" />
309 <when input="input_format" value="bed" format="bed" /> 311 <when input="multiple.input_format" value="bed" format="bed" />
310 <when input="input_format" value="bigwig" format="bigwig" /> 312 <when input="multiple.input_format" value="bigwig" format="bigwig" />
311 <when input="input_format" value="gff" format="gff" /> 313 <when input="multiple.input_format" value="gff" format="gff" />
312 <when input="input_format" value="vcf" format="vcf" /> 314 <when input="multiple.input_format" value="vcf" format="vcf" />
313 <when input="input_format" value="wig" format="bigwig" /> 315 <when input="multiple.input_format" value="wig" format="bigwig" />
314 </change_format> 316 </change_format>
315 </data> 317 </data>
316 318
317 <data format="text" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}"> 319 <data format="text" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}">
318 <filter>input_format in ["bam" , "vcf"]</filter> 320 <filter>input_format in ["bam" , "vcf"]</filter>
319 <change_format> 321 <change_format>
320 <when input="input_format" value="bam" format="bam" /> 322 <when input="multiple.input_format" value="bam" format="bam" />
321 <when input="input_format" value="vcf" format="vcf" /> 323 <when input="multiple.input_format" value="vcf" format="vcf" />
322 </change_format> 324 </change_format>
323 </data> 325 </data>
324 <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}"> 326 <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}">
325 <filter>input_format in ["wig"]</filter> 327 <filter>input_format in ["wig"]</filter>
326 <change_format> 328 <change_format>
327 <when input="input_format" value="wig" format="bedgraph" /> 329 <when input="multiple.input_format" value="wig" format="bedgraph" />
328 </change_format> 330 </change_format>
329 </data> 331 </data>
330 </outputs> 332 </outputs>
331 333
332 <tests> 334 <tests>