Mercurial > repos > iuc > stacks2_refmap

comparison macros.xml @ 4:5e10f396979e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
author iuc
date Wed, 01 Sep 2021 11:31:54 +0000
parents 4f65e343ecdf
children 887e0991eb24
comparison
equal deleted inserted replaced
3:4f65e343ecdf 4:5e10f396979e
8 <yield/> 8 <yield/>
9 </requirements> 9 </requirements>
10 </xml> 10 </xml>
11 11
12 <token name="@STACKS_VERSION@">2.55</token> 12 <token name="@STACKS_VERSION@">2.55</token>
13 <token name="@WRAPPER_VERSION@">0</token> 13 <token name="@WRAPPER_VERSION@">1</token>
14 <token name="@PROFILE@">20.01</token> 14 <token name="@PROFILE@">20.05</token>
15 15
16 <xml name="citation"> 16 <xml name="citation">
17 <citations> 17 <citations>
18 <citation type="doi">10.1111/mec.12354</citation> 18 <citation type="doi">10.1111/mec.12354</citation>
19 <citation type="doi">10.1111/mec.12330</citation> 19 <citation type="doi">10.1111/mec.12330</citation>
422 <expand macro="gstacks_outputs_macro"/> 422 <expand macro="gstacks_outputs_macro"/>
423 <data format="txt" name="distribs" label="${tool.name} on ${on_string} log.distribs" from_work_dir="stacks_outputs/gstacks.log.distribs"> 423 <data format="txt" name="distribs" label="${tool.name} on ${on_string} log.distribs" from_work_dir="stacks_outputs/gstacks.log.distribs">
424 <filter>add_log_distribs</filter> 424 <filter>add_log_distribs</filter>
425 </data> 425 </data>
426 <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments"> 426 <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments">
427 <discover_datasets pattern="(?P&lt;name&gt;.*).alns.bam$" ext="bam" directory="stacks_outputs"/> 427 <discover_datasets pattern="(?P&lt;name&gt;.*).alns.bam$" format="bam" directory="stacks_outputs"/>
428 <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap!=None</filter> 428 <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] and popmap!=None</filter>
429 </collection> 429 </collection>
430 <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam"> 430 <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam">
431 <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap==None</filter> 431 <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] and popmap==None</filter>
432 </data> 432 </data>
433 </xml> 433 </xml>
434 <xml name="gstacks_outputs_macro" token_tooladd=""> 434 <xml name="gstacks_outputs_macro" token_tooladd="">
435 <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites"> 435 <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites">
436 <discover_datasets pattern="(?P&lt;name&gt;catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs"/> 436 <discover_datasets pattern="(?P&lt;name&gt;catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs"/>