| Previous changeset 8:9e3e80cc4ad4 (2020-11-18) Next changeset 10:d10bdad2fd17 (2022-10-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f |
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modified:
unicycler.xml |
| b |
| diff -r 9e3e80cc4ad4 -r 6e26c9afd301 unicycler.xml --- a/unicycler.xml Wed Nov 18 20:26:04 2020 +0000 +++ b/unicycler.xml Sat Sep 24 21:14:02 2022 +0000 |
| [ |
| b'@@ -1,7 +1,11 @@\n-<tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.0" profile="20.09">\n+<tool id="unicycler" name="Create assemblies with Unicycler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">\n <macros>\n- <token name="@VERSION@">0.4.8</token>\n+ <token name="@TOOL_VERSION@">0.5.0</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n </macros>\n+ <xrefs>\n+ <xref type="bio.tools">unicycler</xref>\n+ </xrefs>\n <edam_topics>\n <edam_topic>topic_0196</edam_topic>\n </edam_topics>\n@@ -9,7 +13,8 @@\n <edam_operation>operation_0525</edam_operation>\n </edam_operations>\n <requirements>\n- <requirement type="package" version="@VERSION@">unicycler</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">unicycler</requirement>\n+ <requirement type="package" version="1.15.1">samtools</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n ## Preparing files\n@@ -57,13 +62,10 @@\n #end if\n ln -s \'${long}\' \'$lr\' &&\n #end if\n-## Get location for pilon installation\n-pilon=`pilon --jar_dir` &&\n ## Running Unicycler\n unicycler -t "\\${GALAXY_SLOTS:-4}"\n -o ./\n --verbosity 3\n---pilon_path \\$pilon\n #if str( $paired_unpaired.fastq_input_selector ) == "paired"\n -1 \'$fq1\'\n -2 \'$fq2\'\n@@ -86,7 +88,6 @@\n #end if\n ## Spades Options section\n ## ----------------------------------------------------------\n-$spades.no_correct\n --min_kmer_frac \'$spades.min_kmer_frac\'\n --max_kmer_frac \'$spades.max_kmer_frac\'\n #if str($spades.kmers) != \'\'\n@@ -105,12 +106,6 @@\n #end if\n --start_gene_id \'$rotation.start_gene_id\'\n --start_gene_cov \'$rotation.start_gene_cov\'\n-## Pilon Options section\n-## ----------------------------------------------------------\n-$pilon.no_pilon\n-#if str($pilon.min_polish_size) != \'\'\n- --min_polish_size \'$pilon.min_polish_size\'\n-#end if\n ## Graph cleaning Options sdection\n ## ----------------------------------------------------------\n --min_component_size \'$graph_clean.min_component_size\'\n@@ -124,6 +119,15 @@\n #if str($lr_align.low_score) != \'\'\n --low_score \'$lr_align.low_score\'\n #end if\n+$lr_align.no_simple_bridges\n+--keep $keep\n+#if $keep != \'0\'\n+ && mkdir \'spades_graphs\'\n+ && mv 00*gfa \'./spades_graphs/\'\n+#end if\n+#if $keep == \'2\' and $long\n+ && samtools view -@ "\\${GALAXY_SLOTS:-4}" -u \'read_alignment/long_read_alignments.sam\' | samtools sort -@ "\\${GALAXY_SLOTS:-4}" -o \'read_alignment/long_read_alignments.bam\'\n+#end if\n ]]></command>\n <inputs>\n <conditional name="paired_unpaired">\n@@ -160,8 +164,6 @@\n <param argument="--min_anchor_seg_len" type="integer" min="0" optional="true" label="Unicycler will not use segments shorter than this as scaffolding anchors"/>\n <section name="spades" expanded="False" title="SPAdes options"\n help="Unicycler uses SPAdes to construct assembly graphs. You can modify some of the SPAdes settings here. Use this ONLY if you know what you are doing!">\n- <param argument="--no_correct" type="boolean" checked="false" truevalue="--no_correct" falsevalue=""\n- label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/>\n <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2"\n label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>\n <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95"\n@@ -183,11 +185,6 @@\n <param argument="--start_gene_id" type="float" min="0" max="100" value="90" label="The minimum required BLAST percent identity for a start gene search"/>\n <param argument="--start_gene_cov" type="float" min="0" max="100" value="95" label="The minimum required BLAST percent coverage for a start gene search"/>\n <'..b' </element>\n+ </output_collection>\n+ </test>\n+ <!-- Test keep value = 2 -->\n+ <test expect_num_outputs="4">\n+ <conditional name="paired_unpaired">\n+ <param name="fastq_input_selector" value="paired" />\n+ <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />\n+ <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />\n+ </conditional>\n+ <param name="long" value="onp.fa" ftype="fasta" />\n+ <param name="mode" value="normal" />\n+ <param name="keep" value="2"/>\n+ <output name="assembly_graph" ftype="gfa1">\n+ <assert_contents>\n+ <has_line_matching expression="S\\t1\\t[ATCG]{5386,5386}\\tLN:i:5386\\tdp:f:1.0"/>\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+ <output_collection name="spades_collection" type="list" count="14">\n+ <element name="001_spades_graph_k027">\n+ <assert_contents>\n+ <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output name="bam_file" ftype="bam">\n+ <assert_contents>\n+ <has_size value="2084" delta="100"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Test no simple bridges option -->\n+ <test expect_num_outputs="2">\n+ <conditional name="paired_unpaired">\n+ <param name="fastq_input_selector" value="paired" />\n+ <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />\n+ <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />\n+ </conditional>\n+ <param name="long" value="onp.fa" ftype="fasta" />\n+ <param name="mode" value="normal" />\n+ <param name="keep" value="0"/>\n+ <section name="lr_align">\n+ <param name="no_simple_bridges" value="true"/>\n+ </section>\n <output name="assembly_graph" ftype="gfa1">\n <assert_contents>\n <has_line_matching expression="S\\t1\\t[ATCG]{5386,5386}\\tLN:i:5386\\tdp:f:1.0"/>\n@@ -352,26 +455,9 @@\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="none"/>\n- </conditional>\n- <param name="min_anchor_seg_len" value="10"/>\n- <section name="spades">\n- <param name="kmers" value="21,23"/>\n- </section>\n- <param name="long" value="only_long.fasta" ftype="fasta" />\n- <output name="assembly_graph" ftype="gfa1">\n- <assert_contents>\n- <has_text text="S" />\n- </assert_contents>\n- </output>\n- <output name="assembly" ftype="fasta">\n- <assert_contents>\n- <has_text text=">1" />\n- </assert_contents>\n- </output>\n+ <assert_command>\n+ <has_text text="--no_simple_bridges" />\n+ </assert_command>\n </test>\n </tests>\n <help><![CDATA[\n@@ -436,11 +522,6 @@\n .. _`Hamming graph`: https://en.wikipedia.org/wiki/Hamming_graph\n .. _`Hamming distance`: https://en.wikipedia.org/wiki/Hamming_distance\n \n-This following option turns error correction on and off::\n-\n- --no_correct\n- Skip SPAdes error correction step\n- (default: conduct SPAdes error correction)\n \n -----\n \n' |