Mercurial > repos > iuc > stacks_sstacks
comparison stacks_sstacks.xml @ 12:96de7538bf0c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
| author | iuc |
|---|---|
| date | Fri, 07 Apr 2023 22:05:37 +0000 |
| parents | 563af4497055 |
| children |
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| 11:563af4497055 | 12:96de7538bf0c |
|---|---|
| 1 <tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.0"> | 1 <tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.1"> |
| 2 <description>match stacks to a catalog</description> | 2 <description>match stacks to a catalog</description> |
| 3 <expand macro="bio_tools"/> | |
| 4 <macros> | 3 <macros> |
| 5 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 6 </macros> | 5 </macros> |
| 6 <expand macro="bio_tools"/> | |
| 7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 8 <expand macro="stdio"/> | 8 <expand macro="stdio"/> |
| 9 <command><![CDATA[ | 9 <command><![CDATA[ |
| 10 #import re | 10 #import re |
| 11 | 11 |
| 33 #set $filename = str($input_file.element_identifier) | 33 #set $filename = str($input_file.element_identifier) |
| 34 #if not filename.endswith('.tsv') | 34 #if not filename.endswith('.tsv') |
| 35 #set $filename = $filename + ".tsv" | 35 #set $filename = $filename + ".tsv" |
| 36 #end if | 36 #end if |
| 37 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename) | 37 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename) |
| 38 ln -s '${input_file}' 'stacks_inputs/$filename' && | 38 ## When using a popmap, stacks write to the input dir (see also below) |
| 39 #if $popmap | |
| 40 cp '${input_file}' 'stacks_inputs/$filename' && | |
| 41 #else | |
| 42 ln -s '${input_file}' 'stacks_inputs/$filename' && | |
| 43 #end if | |
| 39 | 44 |
| 40 #if $filename.endswith('.tags.tsv') | 45 #if $filename.endswith('.tags.tsv') |
| 41 #set samples += " -s 'stacks_inputs/"+$filename[:-9] + "'" | 46 #set samples += " -s 'stacks_inputs/"+$filename[:-9] + "'" |
| 42 #end if | 47 #end if |
| 43 #end if | 48 #end if |
| 80 <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" /> | 85 <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" /> |
| 81 <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/pstacks" /> | 86 <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/pstacks" /> |
| 82 | 87 |
| 83 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" /> | 88 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" /> |
| 84 | 89 |
| 85 <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" /> | 90 <param argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" /> |
| 86 | 91 |
| 87 <param name="check_haplo" argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Don't verify haplotype of matching locus" /> | 92 <param name="check_haplo" argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Don't verify haplotype of matching locus" /> |
| 88 | 93 |
| 89 <param name="gapped" argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" /> | 94 <param argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" /> |
| 90 </inputs> | 95 </inputs> |
| 91 | 96 |
| 92 <outputs> | 97 <outputs> |
| 93 <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" /> | 98 <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" /> |
| 94 | 99 |