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comparison macros.xml @ 1:7e2debc267eb draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"
author jjohnson
date Mon, 06 Jan 2020 15:18:20 -0500
parents b59ae99e47d4
children cb2fc9f60381
comparison
equal deleted inserted replaced
0:b59ae99e47d4 1:7e2debc267eb
253 --warn_sim $warning.warn_sim 253 --warn_sim $warning.warn_sim
254 --warn_aln $warning.warn_aln 254 --warn_aln $warning.warn_aln
255 #end if 255 #end if
256 ]]></token> 256 ]]></token>
257 257
258 <xml name="select_outputs"> 258 <xml name="select_outputs">
259 </xml> 259 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">
260 <option value="log" selected="true">log</option>
261 <option value="warnings" selected="true">Warnings</option>
262 <option value="Primary_clustering_dendrogram" selected="true">Primary_clustering_dendrogram.pdf</option>
263 <option value="Secondary_clustering_dendrograms">Secondary_clustering_dendrograms.pdf</option>
264 <option value="Secondary_clustering_MDS">Secondary_clustering_MDS.pdf</option>
265 <option value="Clustering_scatterplots" selected="true">Clustering_scatterplots.pdf</option>
266 <yield/>
267 </param>
268 </xml>
269 <xml name="select_drep_outputs">
270 <expand macro="select_outputs">
271 <option value="Cluster_scoring">Cluster_scoring.pdf</option>
272 <option value="Winning_genomes">Winning_genomes.pdf</option>
273 <option value="Widb">Widb.csv</option>
274 <option value="Chdb">Chdb.tsv</option>
275 </expand>
276 </xml>
260 277
261 <xml name="common_outputs"> 278 <xml name="common_outputs">
262 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/logger.log"/> 279 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/logger.log">
263 <data name="warnings" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/warnings.txt"/> 280 <filter>'log' in select_outputs or not select_outputs</filter>
264 <data name="Primary_clustering_dendrogram" format="pdf" label="${tool.name} on ${on_string}: Primary_clustering_dendrogram.pdf" from_work_dir="outdir/figures/Primary_clustering_dendrogram.pdf"/> 281 </data>
265 <data name="Secondary_clustering_dendrograms" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_dendrograms.pdf" from_work_dir="outdir/figures/Secondary_clustering_dendrograms.pdf"/> 282 <data name="warnings" format="txt" label="${tool.name} on ${on_string}: Warnings" from_work_dir="outdir/log/warnings.txt">
266 <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf"/> 283 <filter>'warnings' in select_outputs</filter>
267 <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf"/> 284 </data>
268 </xml> 285 <data name="Primary_clustering_dendrogram" format="pdf" label="${tool.name} on ${on_string}: Primary_clustering_dendrogram.pdf" from_work_dir="outdir/figures/Primary_clustering_dendrogram.pdf">
269 <xml name="common_outputs2"> 286 <filter>'Primary_clustering_dendrogram' in select_outputs</filter>
287 </data>
288 <data name="Secondary_clustering_dendrograms" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_dendrograms.pdf" from_work_dir="outdir/figures/Secondary_clustering_dendrograms.pdf">
289 <filter>'Secondary_clustering_dendrograms' in select_outputs</filter>
290 </data>
291 <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf">
292 <filter>'Secondary_clustering_MDS' in select_outputs</filter>
293 </data>
294 <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf">
295 <filter>'Clustering_scatterplots' in select_outputs</filter>
296 </data>
297 </xml>
298
299
300 <xml name="drep_outputs">
301 <expand macro="common_outputs"/>
302 <data name="Cluster_scoring" format="pdf" label="${tool.name} on ${on_string}: Cluster_scoring.pdf" from_work_dir="outdir/figures/Cluster_scoring.pdf">
303 <filter>'Cluster_scoring' in select_outputs</filter>
304 </data>
305 <data name="Winning_genomes" format="pdf" label="${tool.name} on ${on_string}: Winning_genomes.pdf" from_work_dir="outdir/figures/Winning_genomes.pdf">
306 <filter>'Winning_genomes' in select_outputs</filter>
307 </data>
308 <data name="Widb" format="csv" label="${tool.name} on ${on_string}: Widb.csv" from_work_dir="outdir/data_tables/Widb.csv">
309 <filter>'Widb' in select_outputs</filter>
310 </data>
311 <data name="Chdb" format="tabular" label="${tool.name} on ${on_string}: Chdb.tsv" from_work_dir="outdir/data/checkM/checkM_outdir/Chdb.tsv">
312 <filter>'Chdb' in select_outputs</filter>
313 </data>
270 </xml> 314 </xml>
271 315
272 <token name="@GENOMES_HELP@"><![CDATA[ 316 <token name="@GENOMES_HELP@"><![CDATA[
273 I/O PARAMETERS: 317 I/O PARAMETERS:
274 -g [GENOMES [GENOMES ...]], --genomes [GENOMES [GENOMES ...]] 318 -g [GENOMES [GENOMES ...]], --genomes [GENOMES [GENOMES ...]]