| Previous changeset 6:14ddfc8ffb93 (2022-01-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 64421702fce231e2fb05bd2f585679154c3e2140 |
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modified:
megahit_wrapper.xml |
| b |
| diff -r 14ddfc8ffb93 -r a96f3ad4e0d8 megahit_wrapper.xml --- a/megahit_wrapper.xml Sun Jan 09 16:57:44 2022 +0000 +++ b/megahit_wrapper.xml Tue Nov 28 07:47:49 2023 +0000 |
| [ |
| b'@@ -1,17 +1,20 @@\n-<?xml version=\'1.0\' encoding=\'utf-8\'?>\n-<tool id="megahit" name="MEGAHIT" version="@TOOL_VERSION@+galaxy0">\n+<tool id="megahit" name="MEGAHIT" version="@TOOL_VERSION@+galaxy1">\n <description>for metagenomics assembly</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">1.2.9</token>\n+ </macros>\n <xrefs>\n <xref type="bio.tools">megahit</xref>\n </xrefs>\n- <macros>\n- <token name="@TOOL_VERSION@">1.2.9</token>\n- </macros>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">megahit</requirement>\n </requirements>\n <version_command>megahit --version</version_command>\n <command detect_errors="exit_code"><![CDATA[\n+if [[ -n "\\$GALAXY_MEMORY_MB" ]]; then\n+ MEMORY="-m \\$((GALAXY_MEMORY_MB * 1024))";\n+fi;\n+\n megahit\n --num-cpu-threads \\${GALAXY_SLOTS:-4}\n #if $input_option.choice == \'paired\'\n@@ -52,6 +55,7 @@\n ${advanced_section.nolocal}\n ${advanced_section.kmin1pass}\n --min-contig-len \'${output_section.min_contig_len}\'\n+ \\$MEMORY\n && cat megahit_out/log\n ]]></command>\n <inputs>\n@@ -88,36 +92,36 @@\n </when>\n </conditional>\n <section name="basic_section" title="Basic assembly options" expanded="True">\n- <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers" help="(kmin+1)-mer with multiplicity lower than d (default 2, specified by --min-count option) will be discarded. You should be cautious to set d less than 2, which will lead to a much larger and noisy graph. We recommend using the default value 2 for metagenomics assembly. If you want to use MEGAHIT to do generic assemblies, please change this value according to the sequencing depth. (recommend --min-count 3 for >40x)."/>\n+ <param argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers" help="(kmin+1)-mer with multiplicity lower than d (default 2, specified by --min-count option) will be discarded. You should be cautious to set d less than 2, which will lead to a much larger and noisy graph. We recommend using the default value 2 for metagenomics assembly. If you want to use MEGAHIT to do generic assemblies, please change this value according to the sequencing depth. (recommend --min-count 3 for >40x)."/>\n <conditional name="k_mer">\n <param name="k_mer_method" type="select" label="K-mer specification method">\n <option value="klist_method">Specify list</option>\n <option value="klim_method">Specify min, max, and step values</option>\n </param>\n <when value="klist_method">\n- <param name="k_list" argument="--k-list" type="text" value="21,29,39,59,79,99,119,141" label="Comma-separated list of kmer size" help="all must be odd, in the range 15-255, and with increments <= 28"/>\n+ <param argument="--k-list" type="text" value="21,29,39,59,79,99,119,141" label="Comma-separated list of kmer size" help="all must be odd, in the range 15-255, and with increments <= 28"/>\n </when>\n <when value="klim_method"> \n- <param name="k_min" argument="--k-min" type="integer" value="21" label="Minimum kmer size" max="255" help="Must be odd number. For ultra complex metagenomics data such as soil, a larger kmin, say 27, is recommended to reduce the complexity of the de Bruijn graph. Quality trimming is also recommended. For high-depth generic data, large --k-min (25 to 31) is recommended. Smaller --k-step, say 10, is more friendly to low-coverage datasets."/>\n- <param name="k_max" argument="--k-max" type="integer" value="141" label="Maximum kmer size" max="255" help="must be odd number"/>\n- <param name="k_step" argument="--k-step" type="integer" value="12" label="Increment '..b'param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="3" label="Strength of low depth pruning" />\n- <param name="prune_depth" argument="--prune-depth" type="integer" value="2" min="0" label="Remove unitigs with avg kmer depth less than this value" />\n-\t\t\t<param name="disconnect_ratio" argument="--disconnect-ratio" type="float" value="0.1" label="Disconnect unitigs if its depth is less than this ratio times the total depth of itself and its siblings" />\n- <param name="low_local_ratio" argument="--low-local-ratio" type="float" value="0.2" label="Remove unitigs if its depth is less than this ratio times the average depth of the neighborhoods" />\n-\t\t\t<param name="cleaning_rounds" argument="--cleaning-rounds" type="integer" value="5" label="Number of rounds for graph cleanning" />\t \n+ <param argument="--bubble-level" type="integer" value="2" min="0" max="2" label="Intensity of bubble merging (0-2), 0 to disable" />\n+ <param argument="--merge-level" type="text" value="20,0.95" label="Merge complex bubbles of length" />\n+ <param argument="--prune-level" type="integer" value="2" min="0" max="3" label="Strength of low depth pruning" />\n+ <param argument="--prune-depth" type="integer" value="2" min="0" label="Remove unitigs with avg kmer depth less than this value" />\n+\t\t\t<param argument="--disconnect-ratio" type="float" value="0.1" label="Disconnect unitigs if its depth is less than this ratio times the total depth of itself and its siblings" />\n+ <param argument="--low-local-ratio" type="float" value="0.2" label="Remove unitigs if its depth is less than this ratio times the average depth of the neighborhoods" />\n+\t\t\t<param argument="--cleaning-rounds" type="integer" value="5" label="Number of rounds for graph cleanning" />\t \n <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="Disable local assembly" />\n <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="Use 1pass mode to build SdBG of k_min" />\n </section>\n <section name="output_section" title="Output options" expanded="True">\n- <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="Minimum length of contigs to output" />\n+ <param argument="--min-contig-len" type="integer" value="200" label="Minimum length of contigs to output" />\n <param name="show_intermediate_contigs" type="boolean" checked="false" label="Return intermediate contigs?"/>\n </section>\n </inputs>\n@@ -129,7 +133,7 @@\n </collection>\n </outputs>\n <tests>\n- <test>\n+ <test expect_num_outputs="1">\n <conditional name="input_option">\n <param name="choice" value="single"/>\n <param name="single_files" value="refExample.fa" ftype="fasta"/>\n@@ -140,14 +144,14 @@\n </assert_contents>\n </output>\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <conditional name="input_option">\n <param name="choice" value="interleaved"/>\n <param name="interleaved_file" value="interleaved-fq.fa"/>\n </conditional>\n <output name="output" file="interleaved_result.fa"/>\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <conditional name="input_option">\n <param name="choice" value="paired"/>\n <param name="fastq_input1" value="paired-fq1.fa"/>\n@@ -155,7 +159,7 @@\n </conditional>\n <output name="output" file="paired_result.fa"/>\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <conditional name="input_option">\n <param name="choice" value="paired_collection"/>\n <conditional name="batchmode">\n' |