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comparison cuffdiff_wrapper.xml @ 3:9ec1cc10742c draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author devteam
date Tue, 07 Feb 2017 18:38:03 -0500
parents c139f0dd4ee6
children e20b05db0839
comparison
equal deleted inserted replaced
2:c139f0dd4ee6 3:9ec1cc10742c
1 <tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.3"> 1 <tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.4">
2 <description>find significant changes in transcript expression, splicing, and promoter use</description> 2 <description>find significant changes in transcript expression, splicing, and promoter use</description>
3 <requirements>
4 <requirement type="set_environment">CUFFDIFF_SCRIPT_PATH</requirement>
5 <requirement type="package" version="2.2.1">cufflinks</requirement>
6 <requirement type="package" version="2.8.2">cummeRbund</requirement>
7 </requirements>
8 <expand macro="stdio" />
9 <macros> 3 <macros>
10 <import>cuff_macros.xml</import> 4 <import>cuff_macros.xml</import>
11 </macros> 5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="2.8.2">bioconductor-cummerbund</requirement>
8 </expand>
9 <expand macro="stdio" />
12 <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command> 10 <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
13 <command><![CDATA[ 11 <command><![CDATA[
14 cuffdiff 12 cuffdiff
15 --no-update-check 13 --no-update-check
16 --quiet 14 --quiet
34 ## Bias correction? 32 ## Bias correction?
35 #if $bias_correction.do_bias_correction == "Yes": 33 #if $bias_correction.do_bias_correction == "Yes":
36 -b 34 -b
37 #if $bias_correction.seq_source.index_source == "history": 35 #if $bias_correction.seq_source.index_source == "history":
38 ## Custom genome from history. 36 ## Custom genome from history.
39 $bias_correction.seq_source.ref_file 37 '$bias_correction.seq_source.ref_file'
40 #else: 38 #else:
41 ## Built-in genome. 39 ## Built-in genome.
42 "${ bias_correction.seq_source.index.fields.path }" 40 '${bias_correction.seq_source.index.fields.path}'
43 #end if 41 #end if
44 #end if 42 #end if
45 43
46 @CONDITION_LABELS@ 44 @CONDITION_LABELS@
47 45
51 #if $advanced_settings.sAdvanced == "Yes": 49 #if $advanced_settings.sAdvanced == "Yes":
52 #if str($advanced_settings.library_type) != 'auto': 50 #if str($advanced_settings.library_type) != 'auto':
53 --library-type=$advanced_settings.library_type 51 --library-type=$advanced_settings.library_type
54 #end if 52 #end if
55 #if $advanced_settings.mask_file: 53 #if $advanced_settings.mask_file:
56 --mask-file=$advanced_settings.mask_file 54 --mask-file '$advanced_settings.mask_file'
57 #end if 55 #end if
58 #if $advanced_settings.time_series: 56 #if $advanced_settings.time_series:
59 --time-series 57 --time-series
60 #end if 58 #end if
61 --max-mle-iterations=$advanced_settings.max_mle_iterations 59 --max-mle-iterations=$advanced_settings.max_mle_iterations
64 --num-frag-count-draws=$advanced_settings.num_frag_count_draws 62 --num-frag-count-draws=$advanced_settings.num_frag_count_draws
65 --num-frag-assign-draws=$advanced_settings.num_frag_assign_draws 63 --num-frag-assign-draws=$advanced_settings.num_frag_assign_draws
66 --min-reps-for-js-test=$advanced_settings.min_reps_for_js_test 64 --min-reps-for-js-test=$advanced_settings.min_reps_for_js_test
67 #end if 65 #end if
68 ## Inputs. 66 ## Inputs.
69 $gtf_input 67 '$gtf_input'
70 68
71 @CONDITION_SAMPLES@ 69 @CONDITION_SAMPLES@
72 #if $generate_sqlite: 70 #if $generate_sqlite:
73 && 71 &&
74 R --vanilla --no-save -f \$CUFFDIFF_SCRIPT_PATH/cummeRbund.R && mv cummeRbund.sqlite "${output_cummerbund}" 72 R --vanilla --no-save -f '$__tool_directory__/cummeRbund.R' && mv cummeRbund.sqlite '${output_cummerbund}'
75 #end if 73 #end if
76 ]]> 74 ]]>
77 </command> 75 </command>
78 <inputs> 76 <inputs>
79 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/> 77 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>
274 <param name="omit_tabular_output" value="yes" /> 272 <param name="omit_tabular_output" value="yes" />
275 <conditional name="in_type"> 273 <conditional name="in_type">
276 <param name="set_in_type" value="BAM" /> 274 <param name="set_in_type" value="BAM" />
277 <repeat name="conditions"> 275 <repeat name="conditions">
278 <param name="name" value="q1" /> 276 <param name="name" value="q1" />
279 <repeat name="samples"> 277 <param name="samples" value="cuffdiff_in1.sam" ftype="sam" />
280 <param name="sample" value="cuffdiff_in1.sam" ftype="sam" />
281 </repeat>
282 </repeat> 278 </repeat>
283 <repeat name="conditions"> 279 <repeat name="conditions">
284 <param name="name" value="q2" /> 280 <param name="name" value="q2" />
285 <repeat name="samples"> 281 <param name="samples" value="cuffdiff_in2.sam" ftype="sam" />
286 <param name="sample" value="cuffdiff_in2.sam" ftype="sam" />
287 </repeat>
288 </repeat> 282 </repeat>
289 </conditional> 283 </conditional>
290 <param name="fdr" value="0.05" /> 284 <param name="fdr" value="0.05" />
291 <param name="min_alignment_count" value="0" /> 285 <param name="min_alignment_count" value="0" />
292 <param name="do_bias_correction" value="No" /> 286 <param name="do_bias_correction" value="No" />
293 <param name="do_normalization" value="No" /> 287 <param name="do_normalization" value="No" />
294 <param name="multiread_correct" value="No"/> 288 <param name="multiread_correct" value="No"/>
295 <param name="sAdditional" value="No"/> 289 <param name="sAdditional" value="No"/>
296 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite"/> 290 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
297 </test> 291 </test>
298 <test> 292 <test>
299 <!-- 293 <!--
300 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam 294 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
301 --> 295 -->
303 <param name="omit_tabular_output" value="no" /> 297 <param name="omit_tabular_output" value="no" />
304 <conditional name="in_type"> 298 <conditional name="in_type">
305 <param name="set_in_type" value="BAM" /> 299 <param name="set_in_type" value="BAM" />
306 <repeat name="conditions"> 300 <repeat name="conditions">
307 <param name="name" value="q1" /> 301 <param name="name" value="q1" />
308 <repeat name="samples"> 302 <param name="samples" value="cuffdiff_in1.sam" ftype="sam" />
309 <param name="sample" value="cuffdiff_in1.sam" ftype="sam" />
310 </repeat>
311 </repeat> 303 </repeat>
312 <repeat name="conditions"> 304 <repeat name="conditions">
313 <param name="name" value="q2" /> 305 <param name="name" value="q2" />
314 <repeat name="samples"> 306 <param name="samples" value="cuffdiff_in2.sam" ftype="sam" />
315 <param name="sample" value="cuffdiff_in2.sam" ftype="sam" />
316 </repeat>
317 </repeat> 307 </repeat>
318 </conditional> 308 </conditional>
319 <param name="fdr" value="0.05" /> 309 <param name="fdr" value="0.05" />
320 <param name="min_alignment_count" value="0" /> 310 <param name="min_alignment_count" value="0" />
321 <param name="do_bias_correction" value="No" /> 311 <param name="do_bias_correction" value="No" />