Mercurial > repos > matthias > stacks2_cstacks

comparison macros.xml @ 3:61afc5a3cd8e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
author matthias
date Fri, 04 Jan 2019 03:31:18 -0500
parents 8427e904f352
children 924e7889aa05
comparison
equal deleted inserted replaced
2:8427e904f352 3:61afc5a3cd8e
126 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file"> 126 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">
127 <filter>add_log</filter> 127 <filter>add_log</filter>
128 </data> 128 </data>
129 </xml> 129 </xml>
130 130
131 <!-- inputs from previous pipeline steps -->
132 <xml name="input_cat_macro">
133 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" />
134 </xml>
135 <xml name="input_tags_macro">
136 <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks" />
137 </xml>
138 <xml name="input_matches_macro">
139 <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks" />
140 </xml>
141 <xml name="input_aln_macro">
142 <param name="input_aln" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" />
143 </xml>
144
131 145
132 <!-- fastq input --> 146 <!-- fastq input -->
133 <xml name="fastq_input_macro" token_fastq_optional="false"> 147 <xml name="fastq_input_macro" token_fastq_optional="false">
134 <conditional name="input_type"> 148 <conditional name="input_type">
135 <param name="input_type_selector" type="select" label="Short read data from individuals" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"> 149 <param name="input_type_selector" type="select" label="Short read data from individuals" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks">
239 </when> 253 </when>
240 </conditional> 254 </conditional>
241 </xml> 255 </xml>
242 256
243 <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) --> 257 <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) -->
244 <!-- TODO tags, snps, and alleles could go to sub collections --> 258 <!-- TODO tags, snps, and alleles could go to sub collections; same for other tools -->
245 <xml name="ustacks_outputs_macro" token_tooladd=""> 259 <xml name="ustacks_outputs_macro" token_tooladd="">
246 <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Stacks"> 260 <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci per sample">
247 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> 261 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
248 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> 262 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
249 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> 263 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
250 </collection> 264 </collection>
251 </xml> 265 </xml>
252 <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv --> 266 <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv -->
253 <xml name="cstacks_outputs_macro" token_tooladd=""> 267 <xml name="cstacks_outputs_macro" token_tooladd="">
254 <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog"> 268 <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog of loci">
255 <discover_datasets pattern="(?P&lt;name&gt;catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" /> 269 <discover_datasets pattern="(?P&lt;name&gt;catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" />
256 </collection> 270 </collection>
257 </xml> 271 </xml>
258 <!-- sstacks outputs collection containing SAMPLE.matches.tsv --> 272 <!-- sstacks outputs collection containing SAMPLE.matches.tsv -->
259 <xml name="sstacks_outputs_macro" token_tooladd=""> 273 <xml name="sstacks_outputs_macro" token_tooladd="">
261 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" /> 275 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
262 </collection> 276 </collection>
263 </xml> 277 </xml>
264 <!-- tsv2bam outputs collection containing SAMPLE.matches.bam --> 278 <!-- tsv2bam outputs collection containing SAMPLE.matches.bam -->
265 <xml name="tsv2bam_outputs_macro" token_tooladd=""> 279 <xml name="tsv2bam_outputs_macro" token_tooladd="">
266 <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Stacks"> 280 <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci">
267 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.bam$" ext="bam" directory="stacks_outputs" /> 281 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.bam$" ext="bam" directory="stacks_outputs" />
268 </collection> 282 </collection>
269 </xml> 283 </xml>
270 <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz --> 284 <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz -->
271 <xml name="gstacks_outputs_macro" token_tooladd=""> 285 <xml name="gstacks_outputs_macro" token_tooladd="">
272 <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string}"> 286 <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites">
273 <discover_datasets pattern="(?P&lt;name&gt;catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs" /> 287 <discover_datasets pattern="(?P&lt;name&gt;catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs" />
274 <discover_datasets pattern="(?P&lt;name&gt;catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs" /> 288 <discover_datasets pattern="(?P&lt;name&gt;catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs" />
275 </collection> 289 </collection>
276 </xml> 290 </xml>
277 291