| Previous changeset 2:e37014a072e9 (2016-05-31) Next changeset 4:35cb17bd8bf9 (2016-08-08) |
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Commit message:
planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 |
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modified:
spades.xml |
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added:
output_dir/input_dataset.yaml test-data/auto_kmer_output.fa test-data/kmer_33_output.fa test-data/kmer_77_output.fa |
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| diff -r e37014a072e9 -r 6dff6ed33cd7 output_dir/input_dataset.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output_dir/input_dataset.yaml Wed Jul 06 16:01:02 2016 -0400 |
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| @@ -0,0 +1,4 @@ +- left reads: [/tmp/tmpwz6C_M/files/000/dataset_15.dat] + orientation: fr + right reads: [/tmp/tmpwz6C_M/files/000/dataset_16.dat] + type: paired-end |
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| diff -r e37014a072e9 -r 6dff6ed33cd7 spades.xml --- a/spades.xml Tue May 31 15:43:30 2016 -0400 +++ b/spades.xml Wed Jul 06 16:01:02 2016 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="spades" name="spades" version="1.3.1"> +<tool id="spades" name="spades" version="1.3.2"> <description>SPAdes genome assembler for regular and single-cell projects</description> <requirements> <requirement type="package" version="3.8.0">spades</requirement> @@ -24,7 +24,12 @@ $onlyassembler $careful -t \${GALAXY_SLOTS:-16} - -k "$kmers" + + #if str($kmer_choice.auto_kmer_choice) == 'False': + -k "$kmer_choice.kmers" + #else + + #end if #if $cov.state == "auto": --cov-cutoff 'auto' @@ -88,9 +93,13 @@ </param> <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" /> <param name="careful" type="boolean" truevalue="--careful" falsevalue="" checked="True" label="Careful correction?" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." /> - <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." > - - </param> + <conditional name="kmer_choice"> + <param name="auto_kmer_choice" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Automatically choose k-mer values" help="k-mer choices can be chosen by SPAdes instead of being entered manually" /> + <when value="false"> + <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." /> + </when> + <when value="true"> </when> + </conditional> <conditional name="cov"> <param name="state" type="select" label="Coverage Cutoff"> <option value="off">Off</option> @@ -210,11 +219,29 @@ <test> <param name="sc" value="false" /> <param name="careful" value="false" /> - <param name="kmers" value="33,55" /> + <param name="kmers" value="33" /> <param name="lib_type" value="paired_end" /> <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" /> <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" /> - <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> + <output name="out_contigs" file="kmer_33_output.fa" ftype="fasta" compare="re_match" lines_diff="1" /> + </test> + <test> + <param name="sc" value="false" /> + <param name="careful" value="false" /> + <param name="auto_kmer_choice" value="true" /> + <param name="lib_type" value="paired_end" /> + <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" /> + <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" /> + <output name="out_contigs" file="auto_kmer_output.fa" ftype="fasta" compare="re_match" lines_diff="1" /> + </test> + <test> + <param name="sc" value="false" /> + <param name="careful" value="false" /> + <param name="kmers" value="77" /> + <param name="lib_type" value="paired_end" /> + <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" /> + <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" /> + <output name="out_contigs" file="kmer_77_output.fa" ftype="fasta" compare="re_match" lines_diff="1" /> </test> </tests> <help> |
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| diff -r e37014a072e9 -r 6dff6ed33cd7 test-data/auto_kmer_output.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/auto_kmer_output.fa Wed Jul 06 16:01:02 2016 -0400 |
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| @@ -0,0 +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 |
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| diff -r e37014a072e9 -r 6dff6ed33cd7 test-data/kmer_33_output.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kmer_33_output.fa Wed Jul 06 16:01:02 2016 -0400 |
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| @@ -0,0 +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 |
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| diff -r e37014a072e9 -r 6dff6ed33cd7 test-data/kmer_77_output.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kmer_77_output.fa Wed Jul 06 16:01:02 2016 -0400 |
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| @@ -0,0 +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 |