Mercurial > repos > rnateam > graphclust_align_cluster

comparison align_cluster.xml @ 1:953353eacec2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 5fe196bd60c65c884ae1685d4b7fb33119564fa7
author rnateam
date Sun, 28 Oct 2018 18:52:14 -0400
parents c05c83b3ef0f
children 40371e8b6ee2
comparison
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0:c05c83b3ef0f 1:953353eacec2
36 $advanced_opts.param_type.indel 36 $advanced_opts.param_type.indel
37 $advanced_opts.param_type.alifold_consensus_dp 37 $advanced_opts.param_type.alifold_consensus_dp
38 #end if 38 #end if
39 #end if 39 #end if
40 " 40 "
41 && 41 &&
42 R-scape --outdir ./RESULTS/ result.aln.sth && 42 '$__tool_directory__/call_rscape.sh' ./RESULTS/ result.aln.sth &&
43 RNAz --locarnate '$alignment_clustal' > alignment.rnaz.out && 43 RNAz --locarnate '$alignment_clustal' > alignment.rnaz.out &&
44 #if str($genomic_cons_opts.genomic_cons_opts_selector) != "no": 44 #if str($genomic_cons_opts.genomic_cons_opts_selector) != "no":
45 clustal_to_alma.py '$alignment_clustal' $cluster_all && 45 clustal_to_alma.py '$alignment_clustal' $cluster_all &&
46 EvoFoldV2.sh -o alignment.evofold.out '${alignment_clustal}.ama' 46 EvoFoldV2.sh -o alignment.evofold.out '${alignment_clustal}.ama'
47 #if str($genomic_cons_opts.genomic_cons_opts_selector) == "hg38_100way": 47 #if str($genomic_cons_opts.genomic_cons_opts_selector) == "hg38_100way":
160 <data name="rnaz_out" format="txt" from_work_dir="alignment.rnaz.out" label="rnaz.out" /> 160 <data name="rnaz_out" format="txt" from_work_dir="alignment.rnaz.out" label="rnaz.out" />
161 <data name="rscape_out" format="txt" from_work_dir="alignment.sum" label="Rscape.summary" /> 161 <data name="rscape_out" format="txt" from_work_dir="alignment.sum" label="Rscape.summary" />
162 <data name="evofold_out" format="txt" from_work_dir="alignment.evofold.out" label="evofold.out" /> 162 <data name="evofold_out" format="txt" from_work_dir="alignment.evofold.out" label="evofold.out" />
163 <data name="cons_tsv" format="tabular" from_work_dir="conservation_metrics.tsv" label="conservation_metrics.tsv" /> 163 <data name="cons_tsv" format="tabular" from_work_dir="conservation_metrics.tsv" label="conservation_metrics.tsv" />
164 </outputs> 164 </outputs>
165
165 <tests> 166 <tests>
167 <test>
168 <param name="cluster_all_fa" value="cluster3.all.fa"/>
169 <param name="cluster_all" value="cluster3.all"/>
170 <output name="cons_tsv" file="alignment3.cons.tsv" compare="sim_size" delta="0"/>
171 <output name="rscape_out" file="rscape3.out" compare="sim_size" delta="10"/>
172 <output name="structure_png" file="structure3.png" compare="sim_size" />
173 <output name="Rscape_R2R" file="alignment3_R2R.sto.pdf" compare="sim_size" />
174 <output name="alignment_sth" file="alignment3.sth" compare="sim_size" delta="100" />
175 <conditional name="genomic_cons_opts">
176 <param name="genomic_cons_opts_selector" value="no"/>
177 </conditional>
178 <param name="results_top_num" value="5"/>
179 </test>
180
166 <test> 181 <test>
167 <param name="cluster_all_fa" value="cluster1.all.fa"/> 182 <param name="cluster_all_fa" value="cluster1.all.fa"/>
168 <param name="cluster_all" value="cluster1.all"/> 183 <param name="cluster_all" value="cluster1.all"/>
169 <output name="alignment_ps" file="alignment1.ps" compare="sim_size" /> 184 <output name="alignment_ps" file="alignment1.ps" compare="sim_size" />
170 <output name="alignment_png" file="alignment1.png" compare="sim_size" /> 185 <output name="alignment_png" file="alignment1.png" compare="sim_size" />
171 <output name="structure_ps" file="structure1.ps" compare="sim_size" /> 186 <output name="structure_ps" file="structure1.ps" compare="sim_size" />
187 <output name="rscape_out" file="rscape1.out" compare="sim_size" delta="10"/>
172 <output name="structure_png" file="structure1.png" compare="sim_size" /> 188 <output name="structure_png" file="structure1.png" compare="sim_size" />
173 <output name="alignment_sth" file="alignment1.sth" compare="sim_size" delta="100" /> 189 <output name="alignment_sth" file="alignment1.sth" compare="sim_size" delta="100" />
174 <output name="alignment_clustal_out" file="alignment1.clustal" /> 190 <output name="alignment_clustal_out" file="alignment1.clustal" />
175 <output name="Rscape_R2R" file="alignment1_R2R.sto.pdf" compare="sim_size" /> 191 <output name="Rscape_R2R" file="alignment1_R2R.sto.pdf" compare="sim_size" />
176 <output name="rnaz_out" file="alignment1.rnaz.out" compare="sim_size" delta="10"/> 192 <output name="rnaz_out" file="alignment1.rnaz.out" compare="sim_size" delta="10"/>
208 <conditional name="bed_opts"> 224 <conditional name="bed_opts">
209 <param name="bed_opts_selector" value="yes"/> 225 <param name="bed_opts_selector" value="yes"/>
210 <param name="transcript_loci_fasta" value="alignment2b-transcript.fa"/> 226 <param name="transcript_loci_fasta" value="alignment2b-transcript.fa"/>
211 <param name="transcript_loci_bed" value="chr7 27162434 27166719 Hoxa9-Xtend5UTR 2 -"/> 227 <param name="transcript_loci_bed" value="chr7 27162434 27166719 Hoxa9-Xtend5UTR 2 -"/>
212 </conditional> 228 </conditional>
213 </test> 229 </test>
214 </tests> 230 </tests>
215 <help> 231 <help>
216 <![CDATA[ 232 <![CDATA[
217 Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. 233 Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.
218 234