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comparison crossmap.xml @ 0:bfcdabc062ca draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
author yhoogstrate
date Wed, 26 Aug 2015 11:04:47 -0400
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1 <tool id="crossmap" name="CrossMap" version="0.2.a">
2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
3
4 <requirements>
5 <requirement type="package" version="312">ucsc_tools</requirement>
6 <requirement type="package" version="0.2">crossmap</requirement>
7 </requirements>
8
9 <stdio>
10 <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/>
11 <regex match=".*" source="both" level="log"/>
12 </stdio>
13
14 <version_command>CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
15
16 <command>
17 CrossMap.py
18 ${multiple.input_format.replace("sam","bam")}
19
20 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
21 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
22 "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
23 #else
24 "$multiple.seq_source.input_chain"
25 #end if
26
27 #if $multiple.input_format in ["bam", "sam"]
28 -m $multiple.insert_size
29 -s $multiple.insert_size_stdev
30 -t $multiple.insert_size_fold
31 #end if
32
33 "$multiple.seq_source.input"
34
35 #if $multiple.input_format == "vcf"
36 "$multiple.seq_source.input_fasta"
37 #end if
38
39 #if str($multiple.include_fails) == "True"
40 >
41 #end if
42
43 "$output"
44
45 #if $multiple.input_format in ["bam", "sam"]
46 ; mv "${output}.${multiple.input_format}" "$output"
47 ; mv "${output}.unmap.${multiple.input_format}" "$output_unmapped"
48 #else if $multiple.input_format in ["vcf"]
49 ; mv "${output}" "$output"
50 ; mv "${output}.unmap" "$output_unmapped"
51 #else if $multiple.input_format in ["wig", "bigwig"]
52 ; mv "${output}.bw" "$output"
53 ; mv "${output}.sorted.bgr" "$output2"
54 #end if
55 </command>
56
57 <inputs>
58 <conditional name="multiple">
59 <param name="input_format" type="select" label="Convert a file of the following format">
60 <option value="bam">BAM</option>
61 <option value="sam">SAM</option>
62 <option value="bed">BED or BED-like</option>
63 <option value="bigwig">BigWig</option>
64 <option value="gff">GFF or GTF</option>
65 <option value="vcf">VCF</option>
66 <option value="wig">Wiggle or bedGraph</option>
67 </param>
68 <when value="bam">
69 <conditional name="seq_source">
70 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
71 <option value="cached">Local data (in galaxy)</option>
72 <option value="history">From History</option>
73 </param>
74 <when value="cached">
75 <param type="data" format="bam" name="input" label="BAM/SAM file">
76 <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." />
78 </param>
79 <param name="input_chain" type="select" label="Lift Over To">
80 <options from_file="liftOver.loc">
81 <column name="name" index="1"/>
82 <column name="value" index="2"/>
83 <column name="dbkey" index="0"/>
84 <filter type="data_meta" ref="input" key="dbkey" column="0" />
85 </options>
86 </param>
87 </when>
88 <when value="history">
89 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
90 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
91 </when>
92 </conditional>
93
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]" />
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]" />
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]" />
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 </conditional>
303 </inputs>
304
305 <outputs>
306 <data format="text" name="output" label="${tool.name} on ">
307 <change_format>
308 <when input="multiple.input_format" value="bam" format="bam" />
309 <when input="multiple.input_format" value="sam" format="sam" />
310 <when input="multiple.input_format" value="bed" format="bed" />
311 <when input="multiple.input_format" value="bigwig" format="bigwig" />
312 <when input="multiple.input_format" value="gff" format="gff" />
313 <when input="multiple.input_format" value="vcf" format="vcf" />
314 <when input="imultiple.nput_format" value="wig" format="bigwig" />
315 </change_format>
316 </data>
317
318 <data format="text" name="output_unmapped" label="${tool.name} unmapped on ">
319 <filter>input_format in ["bam" , "vcf"]</filter>
320 <change_format>
321 <when input="multiple.input_format" value="bam" format="bam" />
322 <when input="multiple.input_format" value="vcf" format="vcf" />
323 </change_format>
324 </data>
325 <data format="text" name="output2" label="${tool.name} on ">
326 <filter>input_format in ["wig"]</filter>
327 <change_format>
328 <when input="multiple.input_format" value="wig" format="bedgraph" />
329 </change_format>
330 </data>
331 </outputs>
332
333 <tests>
334 <!-- BAM/SAM -->
335 <test>
336 <param name="input_format" value="sam"/>
337 <param name="index_source" value="history"/>
338 <param name="input" value="test_bam_01_input_a.sam" ftype="sam"/>
339 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
340 <param name="include_fails" value="False"/>
341
342 <output name="output" file="test_bam_01_output_a.sam" compare="diff" lines_diff="4"/>
343 <output name="output_unmapped" file="test_bam_01_output_a.unmap.sam"/>
344 </test>
345
346 <!-- BED -->
347 <test>
348 <param name="input_format" value="bed"/>
349 <param name="index_source" value="history"/>
350 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
351 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
352 <param name="include_fails" value="False"/>
353
354 <output name="output" file="test_bed_01_output_a__only-matches.bed"/>
355 </test>
356 <test>
357 <param name="input_format" value="bed"/>
358 <param name="index_source" value="history"/>
359 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
360 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
361 <param name="include_fails" value="True"/>
362
363 <output name="output" file="test_bed_01_output_a__all.bed"/>
364 </test>
365 <test>
366 <param name="input_format" value="bed"/>
367 <param name="index_source" value="history"/>
368 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
369 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
370 <param name="include_fails" value="False"/>
371
372 <output name="output" file="test_bed_02_output_a__only-matches.bed"/>
373 </test>
374 <test>
375 <param name="input_format" value="bed"/>
376 <param name="index_source" value="history"/>
377 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
378 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
379 <param name="include_fails" value="True"/>
380
381 <output name="output" file="test_bed_02_output_a__all.bed"/>
382 </test>
383
384 <!-- BigWig --><!-- Malfuncioning in CrossMap 0.2, but patched via galaxy toolshed installer -->
385 <test>
386 <param name="input_format" value="bigwig"/>
387 <param name="index_source" value="history"/>
388 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
389 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
390 <param name="include_fails" value="False"/>
391
392 <output name="output" file="test_bigwig_01_output_a.bw"/>
393 <output name="output2" file="test_bigwig_01_output_a.sorted.bgr"/>
394 </test>
395 <!-- GFF -->
396 <test>
397 <param name="input_format" value="gff"/>
398 <param name="index_source" value="history"/>
399 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
400 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
401 <param name="include_fails" value="False"/>
402
403 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
404 </test>
405 <test>
406 <param name="input_format" value="gff"/>
407 <param name="index_source" value="history"/>
408 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
409 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
410 <param name="include_fails" value="True"/>
411
412 <output name="output" file="test_gff_01_output_a__all.gtf"/>
413 </test>
414
415 <!-- VCF -->
416 <test>
417 <param name="input_format" value="vcf"/>
418 <param name="index_source" value="history_all"/>
419 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/>
420 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>
421 <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
422 <param name="include_fails" value="False"/>
423
424 <output name="output" file="test_vcf_01_output.vcf" compare="diff" lines_diff="4"/>
425 <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/>
426 </test>
427 </tests>
428
429 <!-- WIG - Doesn't understand fixedStep -->
430 <test>
431 <param name="input_format" value="wig"/>
432 <param name="index_source" value="history"/>
433 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
434 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
435 <param name="include_fails" value="False"/>
436
437 <output name="output" file="test_wig_01_output_a.bw"/>
438 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
439 </test>
440 <help>
441 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
442 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
443 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
444 and VCF, reading from remote servers and file compression are supported.
445
446 CrossMap bed
447 ------------
448 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
449 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
450 </help>
451
452 <citations>
453 <citation type="doi">10.1093/bioinformatics/btt730</citation>
454 </citations>
455 </tool>