Mercurial > repos > iuc > stacks2_cstacks
comparison macros.xml @ 4:0345dbaaa79b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
| author | iuc |
|---|---|
| date | Wed, 01 Sep 2021 11:30:01 +0000 |
| parents | c207119ba5f6 |
| children | 0cd2df8af811 |
comparison
equal
deleted
inserted
replaced
| 3:c207119ba5f6 | 4:0345dbaaa79b |
|---|---|
| 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 ${on_string} Read alignments"> |
| 427 <discover_datasets pattern="(?P<name>.*).alns.bam$" ext="bam" directory="stacks_outputs"/> | 427 <discover_datasets pattern="(?P<name>.*).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 ${on_string} Assembled contigs and variant sites"> |
| 436 <discover_datasets pattern="(?P<name>catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs"/> | 436 <discover_datasets pattern="(?P<name>catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs"/> |