| Previous changeset 1:f13d0498a199 (2017-09-29) Next changeset 3:c4eac0c7e542 (2018-02-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb |
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modified:
unicycler.xml |
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| diff -r f13d0498a199 -r e92675014ac9 unicycler.xml --- a/unicycler.xml Fri Sep 29 11:03:48 2017 -0400 +++ b/unicycler.xml Tue Nov 28 10:53:47 2017 -0500 |
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| b'@@ -1,188 +1,114 @@\n-<tool id="unicycler" name="Create assemblies with Unicycler" version="0.4.1">\n+<tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.1">\n+ <macros>\n+ <token name="@VERSION@">0.4.1</token>\n+ </macros>\n <requirements>\n- <requirement type="package" version="0.4.1">unicycler</requirement>\n+ <requirement type="package" version="@VERSION@">unicycler</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n-\n- ## Preparing files\n-\n- #if str( $paired_unpaired.fastq_input_selector ) == "paired":\n-\n- #if $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger\'):\n- ln -s \'${paired_unpaired.fastq_input1}\' fq1.fastq &&\n- #elif $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger.gz\'):\n- ln -s \'${paired_unpaired.fastq_input1}\' fq1.fastq.gz &&\n- #end if\n-\n- #if $paired_unpaired.fastq_input2.is_of_type(\'fastqsanger\'):\n- ln -s \'${paired_unpaired.fastq_input2}\' fq2.fastq &&\n- #elif $paired_unpaired.fastq_input2.is_of_type(\'fastqsanger.gz\'):\n- ln -s \'${paired_unpaired.fastq_input1}\' fq2.fastq.gz &&\n- #end if\n-\n- #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection":\n-\n- #if $paired_unpaired.fastq_input1.forward.is_of_type(\'fastqsanger\'):\n- ln -s \'${paired_unpaired.fastq_input1.forward}\' fq1.fastq &&\n- #elif $paired_unpaired.fastq_input1.forward.is_of_type(\'fastqsanger.gz\'):\n- ln -s \'${paired_unpaired.fastq_input1.forward}\' fq1.fastq.gz &&\n- #end if\n-\n- #if $paired_unpaired.fastq_input1.reverse.is_of_type(\'fastqsanger\'):\n- ln -s \'${paired_unpaired.fastq_input1.reverse}\' fq2.fastq &&\n- #elif $paired_unpaired.fastq_input1.reverse.is_of_type(\'fastqsanger.gz\'):\n- ln -s \'${paired_unpaired.fastq_input2.reverse}\' fq2.fastq.gz &&\n- #end if\n-\n- #elif str( $paired_unpaired.fastq_input_selector ) == "single":\n-\n- #if $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger\'):\n- ln -s \'${paired_unpaired.fastq_input1}\' fq.fastq &&\n- #elif $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger.gz\'):\n- ln -s \'${paired_unpaired.fastq_input1}\' fq.fastq.gz &&\n- #end if\n-\n+## Preparing files\n+#if str( $paired_unpaired.fastq_input_selector ) == "paired"\n+ #if $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger\')\n+ #set fq1 = "fq1.fastq"\n+ #elif $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger.gz\')\n+ #set fq1 = "fq1.fastq.gz"\n+ #end if\n+ #if $paired_unpaired.fastq_input2.is_of_type(\'fastqsanger\')\n+ #set fq2 = "fq2.fastq"\n+ #elif $paired_unpaired.fastq_input2.is_of_type(\'fastqsanger.gz\')\n+ #set fq2 = "fq2.fastq.gz"\n+ #end if\n+ ln -s \'${paired_unpaired.fastq_input1}\' $fq1 &&\n+ ln -s \'${paired_unpaired.fastq_input2}\' $fq2 &&\n+#elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"\n+ #if $paired_unpaired.fastq_input1.forward.is_of_type(\'fastqsanger\')\n+ #set fq1 = "fq1.fastq"\n+ #elif $paired_unpaired.fastq_input1.forward.is_of_type(\'fastqsanger.gz\')\n+ #set fq1 = "fq1.fastq.gz"\n #end if\n-\n- ## Get location for pilon installation\n-\n- pilon=`pilon --jar_dir` &&\n-\n- #if $long_reads:\n- #if $long_reads.is_of_type(\'fastqsanger\'):\n- #set lr = "lr.fastq"\n- ln -s \'${long_reads}\' lr.fastq &&\n- #elif $long_reads.is_of_type(\'fastqsanger.gz\'):\n- #set lr = "lr.fastq.gz"\n- ln -s \'${long_reads}\' lr.fastq.gz &&\n- #elif $long_reads.is_of_type(\'fasta\'):\n- #set lr = "lr.fasta"\n- ln -s \'${long_reads}\' lr.fasta &&\n- #end if\n+ #if $paired_unpaired.fastq_input1.reverse.is_of_type(\'fastqsanger\')\n+ #set fq2 = "fq2.fastq"\n+ #elif $paired_unpaired.fastq_input1.reverse.is_of_type(\'fastqsanger.gz\')\n+ #set fq2 = "fq2.fastq.gz"\n #en'..b' <param name="depth_filter" value="0.25"/>\n+ </section>\n+ <section name="rotation">\n+ <param name="no_rotate" value=""/>\n+ <param name="start_gene_id" value="90"/>\n+ <param name="start_gene_cov" value="95"/>\n+ </section>\n+ <section name="pilon">\n+ <param name="no_pilon" value=""/>\n+ <param name="min_polish_size" value="1000"/>\n+ </section>\n+ <section name="graph_clean">\n+ <param name="min_component_size" value="1000"/>\n+ <param name="min_dead_end_size" value="1000"/>\n+ </section>\n+ <section name="lr_align">\n+ <param name="scores" value="3,-6,-5,-2"/>\n+ </section>\n+ <output name="assembly_graph" ftype="txt">\n+ <assert_contents>\n+ <has_text text="TACGGGGAAGGACGTC" />\n+ </assert_contents>\n+ </output>\n+ <output name="assembly" ftype="fasta">\n+ <assert_contents>\n+ <has_text text="length=5386" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <conditional name="paired_unpaired">\n+ <param name="fastq_input_selector" value="paired_collection"/>\n+ <param name="fastq_input1">\n+ <collection type="paired">\n+ <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" />\n+ <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" />\n+ </collection>\n+ </param>\n+ </conditional>\n+ <param name="mode" value="normal" />\n+ <param name="min_fasta_length" value="100"/>\n+ <param name="linear_seqs" value="0"/>\n+ <section name="spades">\n+ <param name="no_correct" value="true"/>\n+ <param name="min_kmer_frac" value="0.2"/>\n+ <param name="max_kmer_frac" value="0.95"/>\n+ <param name="kmer_count" value="10"/>\n+ <param name="depth_filter" value="0.25"/>\n+ </section>\n+ <section name="rotation">\n+ <param name="no_rotate" value=""/>\n+ <param name="start_gene_id" value="90"/>\n+ <param name="start_gene_cov" value="95"/>\n+ </section>\n+ <section name="pilon">\n+ <param name="no_pilon" value="true"/>\n+ <param name="min_polish_size" value="1000"/>\n+ </section>\n+ <section name="graph_clean">\n+ <param name="min_component_size" value="1000"/>\n+ <param name="min_dead_end_size" value="1000"/>\n+ </section>\n+ <section name="lr_align">\n+ <param name="scores" value="3,-6,-5,-2"/>\n+ </section>\n+ <output name="assembly_graph" ftype="txt">\n+ <assert_contents>\n+ <has_text text="TACGGGGAAGGACGTC" />\n+ </assert_contents>\n+ </output>\n+ <output name="assembly" ftype="fasta">\n <assert_contents>\n <has_text text="length=5386" />\n </assert_contents>\n@@ -390,7 +412,7 @@\n \n If you expect your sample to contain linear (non circular) sequences, set this option::\n \n- --expected_linear_seqs EXPECTED_LINEAR_SEQS\n+ --linear_seqs EXPECTED_LINEAR_SEQS\n The expected number of linear (i.e. non-circular)\n sequences in the underlying sequence\n \n@@ -411,6 +433,10 @@\n --kmer_count KMER_COUNT\n Number of k-mer steps to use in\n SPAdes assembly (default: 10)\n+ --depth_filter DEPTH_FILTER\n+ Filter out contigs lower than this fraction \n+ of the chromosomal depth, if doing so does \n+ not result in graph dead ends (default: 0.25)\n \n ----\n \n' |