Mercurial > repos > iuc > roary
diff roary.xml @ 10:9b2b122d0415 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 2652aac9012d0a19c17e06536bb0e300d048bbf5
| author | iuc |
|---|---|
| date | Sun, 11 Aug 2024 20:29:52 +0000 |
| parents | 91887494eb97 |
| children |
line wrap: on
line diff
--- a/roary.xml Wed Nov 24 21:06:31 2021 +0000 +++ b/roary.xml Sun Aug 11 20:29:52 2024 +0000 @@ -1,8 +1,8 @@ -<tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> +<tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description> <macros> <token name="@TOOL_VERSION@">3.13.0</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> </macros> <xrefs> <xref type="bio.tools">roary</xref> @@ -10,7 +10,6 @@ <requirements> <requirement type="package" version="@TOOL_VERSION@">roary</requirement> </requirements> - <command detect_errors="exit_code"><![CDATA[ #import re #set $filenames = list() @@ -23,23 +22,23 @@ #end for roary - -f out - -p \${GALAXY_SLOTS:-1} - -e - -n - -i '$percent_ident' - -cd '$core_diff' - -g '$advanced.maxclust' - $advanced.split_para - -t '$advanced.trans_tab' - -iv '$advanced.mcl' + -f out + -p \${GALAXY_SLOTS:-1} + -e + -z + -n + -i '$percent_ident' + -cd '$core_diff' + -g '$advanced.maxclust' + $advanced.split_para + -t '$advanced.trans_tab' + -iv '$advanced.mcl' - #for $f in $filenames - '$f' - #end for + #for $f in $filenames + '$f' + #end for - ]]> </command> - + ]]></command> <inputs> <conditional name="gff_input"> <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"> @@ -47,16 +46,15 @@ <option value="collection">Collection</option> </param> <when value="individual"> - <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." /> + <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"/> </when> - <when value='collection'> - <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." /> + <when value="collection"> + <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"/> </when> </conditional> - <param name="percent_ident" type="integer" value="95" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" /> - <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." /> - - <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."> + <param name="percent_ident" type="integer" value="95" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches"/> + <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."/> + <param name="outputs" type="select" label="Additional outputs" help="Summary statistics, core gene alignments and Gene Presence/Absence tables are always produced." multiple="true" display="checkboxes"> <option value="abg_nw">Accessory binary genes in newick format</option> <option value="abg_fa">Accessory binary genes in fasta format</option> <option value="accgraph">Accessory graph in dot format</option> @@ -74,20 +72,17 @@ <option value="numuniq_rtab">Number of Unique Genes in Rtab format</option> <option value="pangenomeref">FASTA file which contains a single representative nucleotide sequence from each of the clusters in the pan genome (core and accessory)</option> </param> - <section name="advanced" title="Advanced options" expanded="false"> - <param name="maxclust" type="integer" value="50000" label="Maximum number of clusters" help="The maximum number of clusters to assign proteins" /> - <param name="split_para" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Don't split paralogs" help="Click yes so that paralogs aren't split." /> - <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." /> - <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!" /> + <param name="maxclust" type="integer" value="50000" label="Maximum number of clusters" help="The maximum number of clusters to assign proteins"/> + <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."/> + <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."/> + <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!"/> </section> - </inputs> - <outputs> - <data format="tabular" name="sumstats" label="${tool.name} on ${on_string} Summary statistics" from_work_dir="out/summary_statistics.txt" /> - <data format="fasta" name="core_gene_aln" label="${tool.name} on ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln" /> - <data format="csv" name="gene_p_a" label="${tool.name} on ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv" /> + <data format="tabular" name="sumstats" label="${tool.name} on ${on_string} Summary statistics" from_work_dir="out/summary_statistics.txt"/> + <data format="fasta" name="core_gene_aln" label="${tool.name} on ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln"/> + <data format="csv" name="gene_p_a" label="${tool.name} on ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv"/> <data format="fasta" name="acc_bin" label="${tool.name} on ${on_string} Accessory Binary Genes" from_work_dir="out/accessory_binary_genes.fa"> <filter>outputs and 'abg_fa' in outputs</filter> </data> @@ -137,22 +132,20 @@ <filter>outputs and 'pangenomeref' in outputs</filter> </data> </outputs> - <tests> - <test> - <param name="gff_input_selector" value="individual" /> - <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3" /> - <output name="sumstats" file="out/summary_statistics.txt" ftype="tabular" /> + <test expect_num_outputs="3"> + <param name="gff_input_selector" value="individual"/> + <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3"/> + <output name="sumstats" file="out/summary_statistics.txt" ftype="tabular"/> </test> - <test> - <param name="gff_input_selector" value="individual" /> - <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3" /> - <param name="percent_ident" value="50" /> - <param name="core_diff" value="50.0" /> - <output name="sumstats" file="test2/summary_statistics.txt" ftype="tabular" /> + <test expect_num_outputs="3"> + <param name="gff_input_selector" value="individual"/> + <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3"/> + <param name="percent_ident" value="50"/> + <param name="core_diff" value="50.0"/> + <output name="sumstats" file="test2/summary_statistics.txt" ftype="tabular"/> </test> </tests> - <help><![CDATA[ **Roary** @@ -186,9 +179,7 @@ For further info see: http://sanger-pathogens.github.io/Roary/ ]]> </help> - <citations> <citation type="doi">10.1093/bioinformatics/btv421</citation> </citations> - </tool>