| Previous changeset 6:65c2d63fcbe6 (2017-05-13) Next changeset 8:884dc0264950 (2018-09-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 |
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modified:
spades.xml test-data/kmer_33_output.fa test-data/kmer_77_output.fa |
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| diff -r 65c2d63fcbe6 -r 9006e5836729 spades.xml --- a/spades.xml Sat May 13 15:51:58 2017 -0400 +++ b/spades.xml Mon Oct 30 07:20:13 2017 -0400 |
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| b'@@ -1,7 +1,7 @@\n-<tool id="spades" name="SPAdes" version="3.9.0">\n+<tool id="spades" name="SPAdes" version="3.11.1">\n <description>genome assembler for regular and single-cell projects</description>\n <requirements>\n- <requirement type="package" version="3.9.0">spades</requirement>\n+ <requirement type="package" version="3.11.1">spades</requirement>\n </requirements>\n <stdio>\n <exit_code range="1:" />\n@@ -74,6 +74,21 @@\n && cat scaffolds.fasta | python \'$write_tsv_script\' > \'$out_scaffold_stats\'\n ]]>\n </command>\n+ \n+ <configfiles>\n+ <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python\n+import sys,re\n+search_str = r\'^>(NODE|\\S+)_(\\d+)(?:_|\\s)length_(\\d+)_cov_(\\d+\\.*\\d*).*\\$\'\n+replace_str = r\'\\1_\\2\\t\\3\\t\\4\'\n+cmd = re.compile(search_str)\n+sys.stdout.write(\'#name\\tlength\\tcoverage\\n\')\n+for i,line in enumerate(sys.stdin):\n+ if cmd.match(line):\n+ sys.stdout.write(cmd.sub(replace_str,line))\n+]]>\n+ </configfile>\n+ </configfiles>\n+ \n <inputs>\n <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean">\n <option value="false">No</option>\n@@ -142,38 +157,33 @@\n <param optional="true" format="fasta,fastq" label="Sanger reads" multiple="true" name="sanger_reads" type="data" />\n <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />\n <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />\n+ <param name="contig_graph_out" type="boolean" checked="False" label="Output final assembly graph (contigs)?" help="Will output the final assembly graph (contigs) in fastg format for visualisation" />\n+ <param name="scaffold_graph_out" type="boolean" checked="False" label="Output final assembly graph with scaffolds?" help="Will output the final assembly graph with scaffold information in gfa format for visualisation" />\n </inputs>\n- <configfiles>\n- <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python\n-import sys,re\n-search_str = r\'^>(NODE|\\S+)_(\\d+)(?:_|\\s)length_(\\d+)_cov_(\\d+\\.*\\d*).*\\$\'\n-replace_str = r\'\\1_\\2\\t\\3\\t\\4\'\n-cmd = re.compile(search_str)\n-sys.stdout.write(\'#name\\tlength\\tcoverage\\n\')\n-for i,line in enumerate(sys.stdin):\n- if cmd.match(line):\n- sys.stdout.write(cmd.sub(replace_str,line))\n-]]>\n- </configfile>\n- </configfiles>\n \n <outputs>\n- <data format="tabular" label="SPAdes contig stats" name="out_contig_stats" >\n+ <data format="tabular" label="${tool.name} on ${on_string}: contig stats" name="out_contig_stats" >\n <actions>\n <action name="column_names" type="metadata" default="name,length,coverage"/>\n </actions>\n </data>\n- <data format="tabular" label="SPAdes scaffold stats" name="out_scaffold_stats" >\n+ <data format="tabular" label="${tool.name} on ${on_string}: scaffold stats" name="out_scaffold_stats" >\n <actions>\n <action name="column_names" type="metadata" default="name,length,coverage"/>\n </actions>\n </data>\n- <data format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" name="out_contigs" />\n- <data format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" name="out_scaffolds" />\n- <data format="txt" from_work_dir="spades.log" label="SPAdes log" name="out_log" />\n+ <data format="fasta" from_work_dir="contigs.fasta" label="${tool.name} on ${on_string}: contigs (fasta)" name="out_contigs" />\n+ <data format="fasta" from_work_dir="scaffolds.fasta" label="${tool.name} on ${on_string}: scaffolds (fasta)" name="out_scaffolds" />\n+ <data format="txt" from_work_dir="spades.log" label="${tool.name}'..b' ${on_string}: assembly graph" name="contig_graph">\n+ <filter>contig_graph_out</filter>\n+ </data>\n+ <data format="txt" from_work_dir="assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: assembly graph with scaffolds" name="scaffold_graph">\n+ <filter>scaffold_graph_out</filter>\n+ </data>\n </outputs>\n <tests>\n- <test>\n+ <test> <!-- Test 1 - basic test with k=33 -->\n <param name="sc" value="false" />\n <param name="careful" value="false" />\n <param name="kmers" value="33" />\n@@ -183,11 +193,11 @@\n <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />\n <output name="out_contig_stats">\n <assert_contents>\n- <has_text_matching expression="NODE_1\\t1000\\t225"/>\n+ <has_text_matching expression="NODE_1\\t1000"/>\n </assert_contents>\n </output>\n </test>\n- <test>\n+ <test> <!-- Test 2 - auto k -->\n <param name="sc" value="false" />\n <param name="careful" value="false" />\n <param name="auto_kmer_choice" value="true" />\n@@ -196,7 +206,7 @@\n <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />\n <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />\n </test>\n- <test>\n+ <test> <!-- Test 3 - k=77 -->\n <param name="sc" value="false" />\n <param name="careful" value="false" />\n <param name="kmers" value="77" />\n@@ -205,6 +215,32 @@\n <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />\n <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />\n </test>\n+ <test> <!-- Test 4 - test for extra graph outputs -->\n+ <param name="sc" value="false" />\n+ <param name="careful" value="false" />\n+ <param name="kmers" value="33" />\n+ <param name="lib_type" value="paired_end" />\n+ <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />\n+ <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />\n+ <param name="contig_graph_out" value="true" />\n+ <param name="scaffold_graph_out" value="true" />\n+ <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />\n+ <output name="out_contig_stats">\n+ <assert_contents>\n+ <has_text_matching expression="NODE_1\\t1000"/>\n+ </assert_contents>\n+ </output>\n+ <output name="contig_graph">\n+ <assert_contents>\n+ <has_text text=">EDGE_"/>\n+ </assert_contents>\n+ </output>\n+ <output name="scaffold_graph">\n+ <assert_contents>\n+ <has_text text="NODE_"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n <help>\n <![CDATA[\n@@ -212,7 +248,7 @@\n \n SPAdes \xe2\x80\x93 St. Petersburg genome assembler \xe2\x80\x93 is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.\n \n-This wrapper runs SPAdes 3.9, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage.\n+This wrapper runs SPAdes, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage.\n \n **License**\n \n@@ -231,6 +267,8 @@\n Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.\n \n Nicola Soranzo fixed various bugs.\n+\n+Simon Gladman added fastg optional outputs.\n ]]>\n </help>\n <citations>\n' |
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| diff -r 65c2d63fcbe6 -r 9006e5836729 test-data/kmer_33_output.fa --- a/test-data/kmer_33_output.fa Sat May 13 15:51:58 2017 -0400 +++ b/test-data/kmer_33_output.fa Mon Oct 30 07:20:13 2017 -0400 |
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| @@ -1,18 +1,18 @@ ->NODE_1_length_1000_cov_140.62 -AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC -TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG -TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC -ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT -AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG -CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT -ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC -AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG -GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA -CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG -CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT -AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA -ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC -GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT -GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA -GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC -TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT +>NODE_1_length_1000_cov_225.838676 +AATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAA +GCACCACCAGTTCGCCTTTTTCATTACCGGCGGTGAAACCTGCCATCAGCACCATGTGAT +CAGCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGGTAGATT +CGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACAGTAACGTTGTGAC +CGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCACGGCAAATCA +GCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTT +TTATTTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCT +GGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGG +GTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTT +TGGCGGGGGCAGAGAGGACGGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATAT +CGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACTC +GCATGGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTGTCAGGTGCGGG +CTTTTTTCTGTGTTTCCTGTACGCGTCAGCCCGCACCGTTACCTGTGGTAATGGTGATGG +TGGTGGTAATGGTGGTGCTAATGCGTTTCATGGATGTTGTGTACTCTGTAATTTTTATCT +GTCTGTGCGCTATGCCTATATTGGTTAAAGTATTTAGTGACCTAAGTCAATAAAATTTTA +ATTTACTCACGGCAGGTAACCAGTTCAGAAGCTGCTATCAGACACTCTTTTTTTAATCCA +CACAGAGACATATTGCCCGTTGCAGTCAGAATGAAAAGCT |
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| diff -r 65c2d63fcbe6 -r 9006e5836729 test-data/kmer_77_output.fa --- a/test-data/kmer_77_output.fa Sat May 13 15:51:58 2017 -0400 +++ b/test-data/kmer_77_output.fa Mon Oct 30 07:20:13 2017 -0400 |
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| @@ -1,18 +1,18 @@ ->NODE_1_length_976_cov_64.4594 -GCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTTTTCAT -TACCGGCGGTGAAACCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAA -TACGGCGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCA -GTTTTTCGACCGGATCGATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCA -TAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGC -ACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGA -CGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAA -GTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGG -TTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTTTGGCGGGGGCAGAGAGGACGGTGG -CCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATATCGGCAACACGCAGAAAACGTTCTG -CATTTGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTT -TGGTCGAAAAAAAAAGCCCGCACTGTCAGGTGCGGGCTTTTTTCTGTGTTTCCTGTACGC -GTCAGCCCGCACCGTTACCTGTGGTAATGGTGATGGTGGTGGTAATGGTGGTGCTAATGC -GTTTCATGGATGTTGTGTACTCTGTAATTTTTATCTGTCTGTGCGCTATGCCTATATTGG -TTAAAGTATTTAGTGACCTAAGTCAATAAAATTTTAATTTACTCACGGCAGGTAACCAGT -TCAGAAGCTGCTATCAGACACTCTTTTTTTAATCCACACAGAGACATATTGCCCGTTGCA -GTCAGAATGAAAAGCT +>NODE_1_length_976_cov_64.459399 +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC +TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG +TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC +ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT +AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG +CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT +ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC +AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG +GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA +CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG +CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT +AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA +ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC +GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT +GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA +GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC +TACTCTGCTGCGGTGC |