Galaxy |

Changeset 0:e02e9af2743f (2017-06-23)

Next changeset 1:a9098353ae22 (2017-07-06)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6

added:
roary.xml
test-data/ex1.gff
test-data/ex2.gff
test-data/out/summary_statistics.txt
test-data/test2/summary_statistics.txt

diff -r 000000000000 -r e02e9af2743f roary.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roary.xml Fri Jun 23 07:53:29 2017 -0400

[

b'@@ -0,0 +1,173 @@\n+<tool id="roary" name="Roary" version="0.1.0">\n+ <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>\n+ \n+ <requirements>\n+ <requirement type="package" version="3.8.2">roary</requirement>\n+ </requirements>\n+ \n+ <command detect_errors="exit_code"><![CDATA[\n+ \n+ #for $counter, $gff in enumerate($gff_input.gffs)\n+ cp $gff temp${counter}.gff &&\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+ \n+ temp*.gff\n+ \n+ ]]></command>\n+ \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+ <option value="individual">Individual</option>\n+ <option value="collection">Collection</option>\n+ </param>\n+ <when value="individual">\n+ <param name="gffs" type="data" multiple="true" format="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+ </when>\n+ <when value=\'collection\'>\n+ <param name="gffs" type="data_collection" collection_type="list" format="gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." />\n+ </when>\n+ </conditional>\n+ <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/>\n+ <param name="core_diff" type="float" 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." value="99.0"/>\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+ <option value="abg_fa">Accessory binary genes in fasta format</option>\n+ <option value="accgraph">Accessory graph in dot format</option>\n+ <option value="acchead_embl">Accessory header file in embl format</option>\n+ <option value="acctab">Accessory gene table in tabular format</option>\n+ <option value="blastfreq">Blast Identity Frequency Rtab file</option>\n+ <option value="clust">Clustered proteins file</option>\n+ <option value="coreaccgraph">Core Accessory Graph in dot format</option>\n+ <option value="coreaccembl">Core Accessory table in embl format</option>\n+ <option value="coreacctab">Core Accessory table in tabular format</option>\n+ <option value="genepa_rtab">Gene Presence Absence file in Rtab format</option>\n+ <option value="numcons_rtab">Number of Conserved Genes in Rtab format</option>\n+ <option value="numpangene_rtab">Number of Genes in Pan Genome in Rtab format</option>\n+ <option value="numnew_rtab">Number of New Genes in Rtab format</option>\n+ <option value="numuniq_rtab">Number of Unique Genes in Rtab format</option>\n+ </param>\n+ \n+ <section name="advanced" title="Advanced options" expanded="false">\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" checked="False" truevalue="-s" falsevalue="" label="Don\'t split paralogs" help="Click yes so that paralogs aren\'t split."/>\n+ <p'..b'\n+ <data format="dot" name="core_acc_graph" label="${tool.name} on ${on_string} Core Accessory Graph" from_work_dir="out/core_accessory_graph.dot" >\n+ <filter>outputs and \'coreaccgraph\' in outputs</filter>\n+ </data>\n+ <data format="embl" name="core_acc_embl" label="${tool.name} on ${on_string} Core Accessory EMBL" from_work_dir="out/core_accessory.header.embl" >\n+ <filter>outputs and \'coreaccembl\' in outputs</filter>\n+ </data>\n+ <data format="tabular" name="core_acc_tab" label="${tool.name} on ${on_string} Core Accessory Table" from_work_dir="out/core_accessory.tab" >\n+ <filter>outputs and \'coreacctab\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="gene_p_a_rtab" label="${tool.name} on ${on_string} Gene Presence Absence Rtab" from_work_dir="out/gene_presence_absence.Rtab" >\n+ <filter>outputs and \'genepa_rtab\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="num_cons_rtab" label="${tool.name} on ${on_string} Number of Conserved Genes" from_work_dir="out/number_of_conserved_genes.Rtab" >\n+ <filter>outputs and \'numcons_rtab\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="num_pangene_rtab" label="${tool.name} on ${on_string} Number of Genes in Pan Geneome" from_work_dir="out/number_of_genes_in_pan_genome.Rtab" >\n+ <filter>outputs and \'numpangene_rtab\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="num_new_rtab" label="${tool.name} on ${on_string} Number of New Genes" from_work_dir="out/number_of_new_genes.Rtab" >\n+ <filter>outputs and \'numnew_rtab\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="num_uniq_rtab" label="${tool.name} on ${on_string} Number of Unique Genes" from_work_dir="out/number_of_unique_genes.Rtab" >\n+ <filter>outputs and \'numuniq_rtab\' 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>\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>\n+ </tests>\n+ \n+ <help><![CDATA[\n+**Roary**\n+\n+Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM.\n+\n+To use Roary, select two or more gff3 files OR a collection of gff3 files\n+\n+**Options**: \n+\n+\n+ - Minimum percentage identity for blastp - an integer, default is [95]\n+\n+ \n+ - Percentage of isolates a gene must be in to be core - a float, default is [99.0]\n+ \n+ \n+**Advanced Options**:\n+ \n+ - Maximum number of clusters - integer, default is [50000]\n+\n+ \n+ - Don\'t split paralogs - check box\n+\n+ \n+ - Translation table - which translation table to use, an integer, default is [11]\n+\n+ \n+ - Change the MCL inflation value - a float, default is [1.5]\n+ \n+\n+For further info see: http://sanger-pathogens.github.io/Roary/\n+ \n+ ]]></help>\n+ \n+ <citations>\n+ <citation type="doi">http://doi.org/10.1093/bioinformatics/btv421</citation>\n+ </citations>\n+ \n+</tool>\n\\ No newline at end of file\n'

diff -r 000000000000 -r e02e9af2743f test-data/ex1.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ex1.gff Fri Jun 23 07:53:29 2017 -0400

b'@@ -0,0 +1,271 @@\n+##gff-version 3\n+##sequence-region abc|SC|contig000001 1 15000\n+abc|SC|contig000001\tProdigal:2.60\tCDS\t172\t1131\t.\t-\t0\tID=abc_00001;gene=hly;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:Q2G1X0,protein motif:TIGRFAMs:TIGR01002,protein motif:Pfam:PF07968.6;locus_tag=abc_00001;product=Alpha-toxin,beta-channel forming cytolysin,Leukocidin/Hemolysin toxin family protein;protein_id=gnl|SC|abc_00001\n+abc|SC|contig000001\tProdigal:2.60\tCDS\t1804\t1950\t.\t+\t0\tID=abc_00002;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00002;product=hypothetical protein;protein_id=gnl|SC|abc_00002\n+abc|SC|contig000001\tProdigal:2.60\tCDS\t1934\t2131\t.\t+\t0\tID=abc_00003;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00003;product=hypothetical protein;protein_id=gnl|SC|abc_00003\n+abc|SC|contig000001\tProdigal:2.60\tCDS\t2621\t3337\t.\t-\t0\tID=abc_00004;inference=ab initio prediction:Prodigal:2.60,protein motif:CLUSTERS:PRK13350,protein motif:Pfam:PF02876.11;locus_tag=abc_00004;product=superantigen-like protein,Staphylococcal/Streptococcal toxin%2C beta-grasp domain;protein_id=gnl|SC|abc_00004\n+abc|SC|contig000001\tProdigal:2.60\tCDS\t3445\t4170\t.\t-\t0\tID=abc_00005;gene=speH;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P0C0I6,protein motif:CLUSTERS:PRK13349,protein motif:Pfam:PF02876.11;locus_tag=abc_00005;note=SPE H;product=hypothetical protein,superantigen-like protein,Staphylococcal/Streptococcal toxin%2C beta-grasp domain;protein_id=gnl|SC|abc_00005\n+abc|SC|contig000001\tProdigal:2.60\tCDS\t4265\t4990\t.\t-\t0\tID=abc_00006;inference=ab initio prediction:Prodigal:2.60,protein motif:CLUSTERS:PRK13043,protein motif:Pfam:PF02876.11;locus_tag=abc_00006;product=superantigen-like protein,Staphylococcal/Streptococcal toxin%2C beta-grasp domain;protein_id=gnl|SC|abc_00006\n+abc|SC|contig000001\tProdigal:2.60\tCDS\t5428\t6429\t.\t+\t0\tID=abc_00007;eC_number=2.1.3.3;gene=argF;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P99073,protein motif:CLUSTERS:PRK04284,protein motif:Cdd:COG0078,protein motif:TIGRFAMs:TIGR00658,protein motif:Pfam:PF00185.1;locus_tag=abc_00007;product=Ornithine carbamoyltransferase,ornithine carbamoyltransferase,Ornithine carbamoyltransferase,ornithine carbamoyltransferase,Aspartate/ornithine carbamoyltransferase%2C Asp/Orn binding domain;protein_id=gnl|SC|abc_00007\n+abc|SC|contig000001\tProdigal:2.60\tCDS\t6449\t7384\t.\t+\t0\tID=abc_00008;eC_number=2.7.2.2;gene=arcC1;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:Q7A627,protein motif:CLUSTERS:PRK12353,protein motif:TIGRFAMs:TIGR00746,protein motif:Pfam:PF00696.22;locus_tag=abc_00008;product=Carbamate kinase 1,putative amino acid kinase,carbamate kinase,Amino acid kinase family protein;protein_id=gnl|SC|abc_00008\n+abc|SC|contig000001\tRNAmmer:1.2\trRNA\t7556\t9112\t.\t+\t0\tID=abc_01705;inference=COORDINATES:profile:RNAmmer:1.2;locus_tag=abc_01705;product=16S ribosomal RNA\n+abc|SC|contig000001\tProdigal:2.60\tCDS\t9419\t9646\t.\t+\t0\tID=abc_00010;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010\n+abc|SC|contig000001\tProdigal:2.60\tCDS\t9952\t10899\t.\t-\t0\tID=abc_00011;inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=abc_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011\n+abc|SC|contig000001\tProdigal:2.60\tCDS\t11148\t11336\t.\t+\t0\tID=abc_00012;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012\n+abc|SC|contig000001\tAragorn:1.2.34\ttRNA\t11803\t11878\t.\t-\t0\tID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct)\n+abc|SC|contig000001\tProdigal:2.60\tCDS\t12241\t12375\t.\t+\t0\tID=abc_00014;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00014;product=Gonococca'..b'TC\n+CACAAAGCACAATACACAGAATGAGAAAAAAAGAAAGATCATTAGACAATATGTCATTGA\n+AAAACGCTGAACTACTTTATAAATTTGCCAATAGTATATTTAGCAATGAAAATTAAGAAG\n+AATAATTAGTGAGTTAAATAATTAAAAAACCACGTCTCGATGGACGTGGTTATTTTTTTA\n+AATGTATTTAATTATAGGATTTCGGGCCCCTGAAAAGTCCCTAAAATTTTGAATAGTATC\n+AAAATCTATAGGAATAATATAATAATAAAAATCTCTACGCATGCAAATGGTGAGTGTTAA\n+AAATCTTGGTGTAGTGTTGGTGTAGTTCAGGTGCAGTATAGATGAAATTTGAGCACAAAA\n+TTACTTAATTAAAAATGTATAAACAAGTGTCAGACGCGTGTCAATTGTGTGTCAAAAAAT\n+TCTATGACGAATAAGCATGCTTGTTTTAATTACTGTATTTTCGGGGCTTATGCGGGGGAC\n+GTTTTGGTGACGCATCATACTATATTACTGAAATTCAAAACAAAAAGAGCCCCGTAATCA\n+CGGAACTCTTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTC\n+GAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGCTGAGCTACCAGGACACG\n+TTTAACAACACAAGAATTATTATATCTAAATGAACTTAAATTAGCAATACCTTGTAAATA\n+AAAAATGTTTATATTTTTCACTATTATAGAGCTATTTATCTAAAAAGGTTCAATAAGACT\n+TAAATGCGAATTCAGGCAACTTAATTGTGTTAAATACAGTTTTGAATGCCTAACTGTATT\n+TCTTTTCTCTTTAAAATACAGTTAAGTACATTATAAGATGTTGTGCGGATAAACAAACTA\n+ATTGCATCAAATTTATTTTAAAATAACAACAACAAAACGTTAAGCGAATAACATTTCGGT\n+GATTTAAAAGCTACGCACGTTTTTGTTATCTTCAAATTTAAATTTTAAGGAGTGTTTTCA\n+ATGGAAGGTTTATTTAACGCAATTAAAGATACCGTAACTGCAGCAATTAATAATGATGGC\n+GCAAAATTAGGCACAAGCATTGTGAGCATCGTTGAAAATGGCGTAGGTTTATTAGGTAAA\n+TTATTCGGATTCTAATTTCAATATGTTATGTAAGTAATCAGTATTATTTCAAAGGTGAGG\n+GAGAGATTTAAATGACTGGACTAGCAGAAGCAATCGCAAATACTGTGCAAGCTGCACAAC\n+AACATGATAGTGTGAAATTAGGCACAAGTATCGTAGACATCGTTGCTAACGGTGTGGGTT\n+TACTAGGTAAATTATTTGGATTCTAATATAATAACTAATATTCTTTAAAATAAACTGGGT\n+GAGCATACTTTAATGTTATGCACTCAGTTTATTTTATTTGCAGAAATTTGAGCCTCTGTT\n+AAGATTTAGATACATAGACAATATAGGAGATGGGGAAATTGGGATATAAAAATATTTTGA\n+TAGACTTTGATGATACAATTGTTGATTTTTATGATGCAGAAGAATGGGCGTTTCACTATA\n+TGGCGAATGTTTTTAATCATAAAGCAACAAAGGATGATTTTTTAACATTTAAAAAAATCA\n+ATCACCAACATTGGGAAGCTTTTCAACAAAATAAATTAACGAAGTCTGAAGTATTATCAG\n+AACGATTTGTGAATTACTTCAAACATCATCAAATGGAAGTTGATGGGCATCGTGCAGATG\n+TGTTATTTAGAAATGGATTAGCAGAAGCTAAAGTTAAATACTTTGATCAAACATTAGAAA\n+CAATTGTCGAATTATCGAAAAGACATGATTTATATATTGTTACTAATGGTGTAACCGAAA\n+CGCAAAAGAGAAGGTTAAATCAGACGCCGTTGCATAAATATATTAAAAAGATATTTATAT\n+CTGAGGAAACAGGATATCAAAAACCTAATCCGGAATTTTTTAATTATGTTTTTAATGATA\n+TTGGTGAGGATGAAAGACAGCACTCGATTATAGTTGGAGATTCTTTAACATCTGACATTC\n+TAGGTGGAATCAATGCGGGTATAGCTACTTGCTGGTTTAATTTTAGAGGATTTGATCATA\n+ATCCAGGAATTATACCTGATTATGAAATTAATTCATGGAAACAACTAAATGATATTGTAC\n+GTTAAGACAAATAATTTGAAAATGATTTATATTAGCTTAAGAAAGTAATTGTAAAAACGA\n+CACTACGAAAAGATGCATTTTCATGCTCGTAGTGTCGAATATTATTATCTTATGGTTTCC\n+ACAATAAGACATCATGTCCCTCTATATTTTTAGCTTCCACATCTGTAAATCCATGATGTA\n+AAAAGAAATCCTTAGAATCATTTCTGCCAATGGCTTTAATTGGCATATTGAAACTCTTTG\n+CAAAATCAATCAATTCTGAAGCGTACCCTCTGTTTTGATATTTTGGTAATACTTCTAACT\n+TCCATAATAATATATAATCTTCAAAATCTGGGAAGTAGATTTCTTCGACATCACCTTTTT\n+TTAGTAATGCCATTCTAGCTCCTAATTGATCTCCGACAAATATGCCATAAAATGGTGAAT\n+CTGAACTTGCATCAATCATTTGACCGTTTAACTCATTGACCATGTATAAGTCTTTGTTGC\n+CAAACGCTCTAAAGTTTTCGAATAATTCGTCAGTTTTGTAATTAATTTCAAGACGTTTGA\n+TTTCACTCATATTTATCTACCCCTTATTTGTTTACTACTATTATTATACATTAAACCACT\n+TGTGTTTTTCATTGATTTGAAAATGTAAAACAATGAACATTATAAATTTTCCATGATTAA\n+ATTGATTTTCAAGCCGTAAAATTGTCAATCACCGGTATAGACTTTATACTATAGTTTGTA\n+ATCGCGTACTTAAGGAGAAAAAACATGGACTGTAAAGTAGTTAGTTTAAATGAAAAAGAT\n+CAGTTTATACCAAAAATAAAGAGCAGTGACCCTGTAATAACAGGATTATTTCAATATGAT\n+GCAGCTCAACAAACTAGTTTTGAAAAAAGGATGTCTAAAGAAAATAATGGAAGAGAAGCG\n+GCATTAGCGAATGTTATTCGTGAATATATGAGTGATTTAAAGCTTTCAAATGAACAAGAA\n+TTAAACATACAACATTTAGCTAATGGTTCAAAAGTTGTGATTGGTGGACAACAAGCAGGG\n+CTTTTCGGGGGACCATTGTATACATTCCATAAAATATTTTCAATCATTACTTTATCTAAG\n+GAATTAACGGATACACATAAGCAACAAGTAGTACCAGTTTTTTGGATTGCAGGAGAAGAT\n+CATGATTTCGATGAAGTGAATCATACATTTGTTTATAACGAAAATCATGGGTCGCTGCAT\n+AAGGTTAAATATCATACAATGGAGATGCCAGAGACGACAGTCTCTAGATATTATCCTGAT\n+AAGGCTGAGTTGAAACAAACTTTAAAAACGATGTTCATTCATATGAAAGAAACTGTTCAT\n+ACACAAGGTCTACTGGAGATTTGTGACAGAATTATTGACCAATATGACTCGTGGACTGAT\n+ATGTTTAAAGCACTACTGCATGAAACATTTAAAGCATATGGCGTTCTATTTATAGATGCG\n+CAGTTTGAGCCGTTAAGAAAAATGGAAGCGCCTATGTTTAAAAAGATTTTGAAAAAACAT\n+CAGTTGCTTGATGATGCTTTTAGAGCAACACAACAACGTACTCAAAATCAAGGCTTGAAT\n+GCGATGATACAAACAGATACAAATGTTCATTTATTCTTACATGATGAAAATATGCGCCAA\n+TTAGTTTCGTATGATGGTAAGCATTTTAAATTAAATAAAACAGATAAGACATATATAAAG\n\\ No newline at end of file\n'

diff -r 000000000000 -r e02e9af2743f test-data/ex2.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ex2.gff Fri Jun 23 07:53:29 2017 -0400

diff -r 000000000000 -r e02e9af2743f test-data/out/summary_statistics.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out/summary_statistics.txt Fri Jun 23 07:53:29 2017 -0400

@@ -0,0 +1,5 @@
+Core genes (99% <= strains <= 100%) 15
+Soft core genes (95% <= strains < 99%) 0
+Shell genes (15% <= strains < 95%) 0
+Cloud genes (0% <= strains < 15%) 0
+Total genes (0% <= strains <= 100%) 15

diff -r 000000000000 -r e02e9af2743f test-data/test2/summary_statistics.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2/summary_statistics.txt Fri Jun 23 07:53:29 2017 -0400

@@ -0,0 +1,5 @@
+Core genes (50% <= strains <= 100%) 15
+Soft core genes (49% <= strains < 50%) 0
+Shell genes (15% <= strains < 49%) 0
+Cloud genes (0% <= strains < 15%) 0
+Total genes (0% <= strains <= 100%) 15