| Previous changeset 9:91887494eb97 (2021-11-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 2652aac9012d0a19c17e06536bb0e300d048bbf5 |
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modified:
roary.xml |
| b |
| diff -r 91887494eb97 -r 9b2b122d0415 roary.xml --- a/roary.xml Wed Nov 24 21:06:31 2021 +0000 +++ b/roary.xml Sun Aug 11 20:29:52 2024 +0000 |
| [ |
| b'@@ -1,8 +1,8 @@\n-<tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+<tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">\n <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>\n <macros>\n <token name="@TOOL_VERSION@">3.13.0</token>\n- <token name="@VERSION_SUFFIX@">2</token>\n+ <token name="@VERSION_SUFFIX@">3</token>\n </macros>\n <xrefs>\n <xref type="bio.tools">roary</xref>\n@@ -10,7 +10,6 @@\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">roary</requirement>\n </requirements>\n-\n <command detect_errors="exit_code"><![CDATA[\n #import re\n #set $filenames = list()\n@@ -23,23 +22,23 @@\n #end for\n \n roary\n- -f out\n- -p \\${GALAXY_SLOTS:-1}\n- -e\n- -n\n- -i \'$percent_ident\'\n- -cd \'$core_diff\'\n- -g \'$advanced.maxclust\'\n- $advanced.split_para\n- -t \'$advanced.trans_tab\'\n- -iv \'$advanced.mcl\'\n+ -f out\n+ -p \\${GALAXY_SLOTS:-1}\n+ -e\n+ -z\n+ -n\n+ -i \'$percent_ident\'\n+ -cd \'$core_diff\'\n+ -g \'$advanced.maxclust\'\n+ $advanced.split_para\n+ -t \'$advanced.trans_tab\'\n+ -iv \'$advanced.mcl\'\n \n- #for $f in $filenames\n- \'$f\'\n- #end for\n+ #for $f in $filenames\n+ \'$f\'\n+ #end for\n \n- ]]> </command>\n-\n+ ]]></command>\n <inputs>\n <conditional name="gff_input">\n <param name="gff_input_selector" type="select" label="Individual gff files or a dataset collection" help="Select between individual gff files or a collection of gff files">\n@@ -47,16 +46,15 @@\n <option value="collection">Collection</option>\n </param>\n <when value="individual">\n- <param name="gffs" type="data" multiple="true" min="2" format="gff,gff3" label="select gff inputs to Roary" help="Select the files you wish to send to Roary, must be in gff3 format with the sequence data at the end of the file." />\n+ <param name="gffs" type="data" format="gff,gff3" min="2" label="select gff inputs to Roary" help="Select the files you wish to send to Roary, must be in gff3 format with the sequence data at the end of the file." multiple="true"/>\n </when>\n- <when value=\'collection\'>\n- <param name="gffs" type="data_collection" collection_type="list" format="gff,gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." />\n+ <when value="collection">\n+ <param name="gffs" type="data_collection" format="gff,gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." collection_type="list"/>\n </when>\n </conditional>\n- <param name="percent_ident" type="integer" value="95" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" />\n- <param name="core_diff" type="float" value="99.0" label="percentage of isolates a gene must be in to be core" help="The total percentage of the isolates that must have the gene for it to be considered a core gene." />\n-\n- <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs" help="Summary statistics, core gene alignments and Gene Presence/Absence tables are always produced.">\n+ <param name="percent_ident" type="integer" value="95" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches"/>\n+ <param name="core_diff" type="float" value="99.0" label="percentage of isolates a gene must '..b' RNA translation table to use. Roary is designed for prokaryotes and so tables 1, 4 or 11 will work, others could be problematic." />\n- <param name="mcl" type="float" value="1.5" label="MCL inflation value" help="This is an advanced setting, change only if you know what you are doing and then at your own risk!" />\n+ <param name="maxclust" type="integer" value="50000" label="Maximum number of clusters" help="The maximum number of clusters to assign proteins"/>\n+ <param name="split_para" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Don\'t split paralogs" help="Click yes so that paralogs aren\'t split."/>\n+ <param name="trans_tab" type="integer" value="11" label="Translation table to use [1 or 4 or 11]" help="DNA -> RNA translation table to use. Roary is designed for prokaryotes and so tables 1, 4 or 11 will work, others could be problematic."/>\n+ <param name="mcl" type="float" value="1.5" label="MCL inflation value" help="This is an advanced setting, change only if you know what you are doing and then at your own risk!"/>\n </section>\n-\n </inputs>\n-\n <outputs>\n- <data format="tabular" name="sumstats" label="${tool.name} on ${on_string} Summary statistics" from_work_dir="out/summary_statistics.txt" />\n- <data format="fasta" name="core_gene_aln" label="${tool.name} on ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln" />\n- <data format="csv" name="gene_p_a" label="${tool.name} on ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv" />\n+ <data format="tabular" name="sumstats" label="${tool.name} on ${on_string} Summary statistics" from_work_dir="out/summary_statistics.txt"/>\n+ <data format="fasta" name="core_gene_aln" label="${tool.name} on ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln"/>\n+ <data format="csv" name="gene_p_a" label="${tool.name} on ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv"/>\n <data format="fasta" name="acc_bin" label="${tool.name} on ${on_string} Accessory Binary Genes" from_work_dir="out/accessory_binary_genes.fa">\n <filter>outputs and \'abg_fa\' in outputs</filter>\n </data>\n@@ -137,22 +132,20 @@\n <filter>outputs and \'pangenomeref\' in outputs</filter>\n </data>\n </outputs>\n-\n <tests>\n- <test>\n- <param name="gff_input_selector" value="individual" />\n- <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3" />\n- <output name="sumstats" file="out/summary_statistics.txt" ftype="tabular" />\n+ <test expect_num_outputs="3">\n+ <param name="gff_input_selector" value="individual"/>\n+ <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3"/>\n+ <output name="sumstats" file="out/summary_statistics.txt" ftype="tabular"/>\n </test>\n- <test>\n- <param name="gff_input_selector" value="individual" />\n- <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3" />\n- <param name="percent_ident" value="50" />\n- <param name="core_diff" value="50.0" />\n- <output name="sumstats" file="test2/summary_statistics.txt" ftype="tabular" />\n+ <test expect_num_outputs="3">\n+ <param name="gff_input_selector" value="individual"/>\n+ <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3"/>\n+ <param name="percent_ident" value="50"/>\n+ <param name="core_diff" value="50.0"/>\n+ <output name="sumstats" file="test2/summary_statistics.txt" ftype="tabular"/>\n </test>\n </tests>\n-\n <help><![CDATA[\n **Roary**\n \n@@ -186,9 +179,7 @@\n For further info see: http://sanger-pathogens.github.io/Roary/\n \n ]]> </help>\n-\n <citations>\n <citation type="doi">10.1093/bioinformatics/btv421</citation>\n </citations>\n-\n </tool>\n' |